SHELXL-93 --------- SHELXL-93 is a FORTRAN-77 program for the refinement of crystal structures from diffraction data, and is primarily designed for single crystal X-ray data at atomic resolution. It is intended to be easy to install and use on a wide variety of computers, and replaces the structure-refining part of SHELX-76. SHELXL-93 is general and efficient for all space groups in all settings and there are no arbitrary limits to the size of problems which can be handled, except for the total memory available to the program. All instructions are in machine independent free format, with extensive use of default settings to minimize the amount of input required from the user. Instructions and data are taken from two standard (ASCII) text files, so that input files can easily be transferred between different computers. SHELXL-93 is provided in source form as well as precompiled PC versions. An application form is reproduced in Appendix F. The program is available free to academics (and for a modest license fee to commercial institutions) subject to the condition that it is acknowledged in all publications which report structures refined with it. SHELXL-93 has been designed particularly for optimum performance on computers with vector and pipelined architectures, and most vectorizing compilers achieve a high degree of vectorization for all important routines without special action on the part of the user. The rate-determining routines are provided in a separate file so that they may be compiled with full optimization; it may well prove counter-productive to optimize or vectorize the rest of the program! The distribution and installation of the program is discussed further in Appendix E. Two auxiliary programs are provided for use with SHELXL-93. PDBINS reads a PDB-format file for a protein and interactively generates a SHELXL-93 '.ins' input file, and CIFTAB reads the '.cif' output file from SHELXL-93 and produces various tables. Users are encouraged to adapt CIFTAB and PDBINS to local circumstances. PDBINS and CIFTAB are described in Appendices B and C respectively. PROGRAM AND FILE ORGANIZATION The way of running SHELXL-93 and the conventions for filenames will of course vary for different computers and operating systems, but the following general concept should be adhered to as much as possible. SHELXL-93 may be run on-line by means of the command: shelxl name where 'name' defines the first component of the filename for all files which correspond to a particular crystal structure. On some systems, 'name' may not be longer than 8 characters. Batch operation will normally require the use of a short batch file containing the above command etc. Before starting SHELXL-93, two ASCII input files must be prepared. The file 'name.ins' contains instructions, crystal and atom data etc. The reflection data file 'name.hkl' contains one line per reflection in the same fixed format as for SHELX-76; batch numbers, wavelength (for Laue data) and 'direction cosines' (for absorption corrections using SHELXA) are optional. Although both files are essentially upwardly compatible with SHELX-76 and the Siemens SHELXTL system, there are many new facilities and some important philosophical differences. When converting '.ins' files from these programs to SHELXL-93, it is a good idea to DELETE or modify all WGHT, OMIT, BLOC, ILSF and MERG instructions (because of changes in their specifications), to review all AFIX instructions for possible differences or more appropriate new options, and to free any coordinates which have been fixed to anchor the molecule in polar space groups (the program has a better way of doing this). The Fourier grid is now larger and the asymmetric unit is found automatically, so FMAP and GRID should be replaced by e.g. 'FMAP 2'. Free variables are no longer required for special position constraints or handling multiply occupied sites (see EXYZ and EADP) but are still legal and are interpreted in the same way. Disordered groups will probably require the addition of PART instructions and may benefit from some of the new restraints (SAME, SADI, FLAT, DELU and SIMU etc.). A brief summary of the progress of the structure refinement appears on the console (i.e. the standard FORTRAN output), and a full listing is written to a file 'name.lst', which can be printed or examined with a text editor. After each refinement cycle a file 'name.res' is (re)written; it is similar to 'name.ins', but has updated values for all refined parameters. It may be copied or edited to name.ins for the next refinement run. Optionally further files 'name.cif' (refinement results) and 'name.fcf' (reflection data) may be created (using the ACTA instruction) in CIF format for direct publication, archiving and input to other programs (e.g. CIFTAB - see Appendices C and D). Two mechanisms are provided for interaction with a SHELXL-93 job which is already running. The first, which it is not possible to implement on all computer systems, applies to 'on-line' runs. If the key combination is hit, the job terminates almost immediately, but without the loss of output buffers etc. which can happen with etc. Usually the key may be used as an alternative to . If the key is hit during least- squares refinement, the program completes the current cycle and then, instead of further refinement cycles, continues with the final structure-factor calculation, tables and Fourier etc. Otherwise has no effect. On computer consoles with no key, or usually have the same effect. The second mechanism requires the user to create the file 'name.fin' (the contents of this file are irrelevant); the program tries at regular intervals to delete it, and if it succeeds it takes the same action as after . The name.fin file is also deleted (if found) at the start of a job in case it has been accidentally left over from a previous job. This approach may be used with batch jobs under most operating systems. The UNIX version of SHELXL-93 is able to read the '.ins' and '.hkl' files in either UNIX or DOS format, and writes the '.res', '.cif' and '.fcf' files in DOS format, so that PC's can access such files via a shared disk without the need for conversion programs such as DOS2UNIX etc. The program may be compiled without this option if necessary. For reasons of efficiency the '.lst' file is always in the local format. Note that for UNIX systems all filenames associated with SHELXL-93 should be in lower case. The program uses two large arrays A and B dynamically, so the limits on the size of structure which can be handled are determined by the dimensions of these two arrays and also of the array C; A, B and C are defined as separate COMMON blocks. The standard version of the program is dimensioned for up to 1500 parameters in each full-matrix block and roughly 5000 atoms (assuming a generous number of restraints etc.), and is suitable for a typical (UNIX) workstation (or mainframe) with 8MB or more physical memory. The standard precompiled PC version is similarly dimensioned but will automatically run as a virtual memory program if less memory is available; it thus requires 8MB of free contiguous disk space (plus another 2MB or so for scratch files) and an 80586, 80486 or 80386/80387 processor. A real mode precompiled PC version PCSHELXL.EXE is also available which should run on virtually ANY PC with a coprocessor and 640K memory; however it is restricted to 300 full-matrix parameters and is somewhat slower. It may be necessary to redimension A, B and C and recompile the program for specific installations, e.g. to fit within a given job category on a mainframe. The highest elements of A and B actually used for the various calculations are printed out by the program (after 'Memory required ='). The program will try to use all available physical (and virtual) memory rather than performing its own disk I/O, thereby achieving longer vector 'runs', which enhances performance on vector and pipelined systems. In some cases, e.g. when a large structure is refined on a MicroVAX or PC with limited physical memory (or allocation of physical memory to a given process in the case of the VAX) this strategy may cause excessive 'paging' and disk I/O. If this happens, the maximum vector run length can be reduced by setting the 4th parameter on the L.S. instruction or by reducing the value of the variable IV in the main program and recompiling; it may also be more efficient to 'block' the refinement or use the CGLS option. THE '.ins' INSTRUCTION FILE - GENERAL ORGANIZATION All instructions commence with a four (or fewer) character word (which may be an atom name); numbers and other information follow in free format, separated by one or more spaces. Upper and lower case input may be freely mixed; with the exception of the text string input using TITL, the input is converted to upper case for internal use in SHELXL-93. The TITL, CELL, ZERR, LATT (if required), SYMM (if required), SFAC, DISP (if required) and UNIT instructions must be given in that order; all remaining instructions, atoms, etc. should come between UNIT and the last instruction, which is always HKLF (to read in reflection data). There is also a facility (which may not be possible under some operating systems) for reading instructions from (possibly nested) 'include files' by inserting the line '+filename' at the appropriate place in the '.ins' file. A number of instructions allow atom names to be referenced; use of such instructions without any atom names means 'all non-hydrogen atoms' (in the current residue, if one has been defined). A list of atom names may also be abbreviated to the first atom, the symbol '>' (separated by spaces), and then the last atom; this means 'all atoms between and including the two named atoms but excluding hydrogens'. For further details of the atom list syntax, see 'RESI' as well as the following examples. EXAMPLES OF SHELXL-93 STRUCTURE REFINEMENTS The two test structures supplied with the program are intended to provide a good illustration of routine structure refinement with SHELXL-93. The output discussed here should not differ significantly from that of the test jobs, except that it has been abbreviated and there may be slight differences in the last decimal place caused by rounding errors. ============================================================================== FIRST EXAMPLE (ags4): The first example (provided as the files 'ags4.ins' and 'ags4.hkl') is the final refinement job for the polymeric inorganic structure Ag(NCSSSSCN)2 AsF6. This structure is described by H.W. Roesky, T. Gries, J. Schimkowiak and P.G. Jones in Angew. Chem. 98 (1986) 93-94 [Int. Edn. 25 (1986) 84-85] and was also used as the cover picture for the SHELXS-86 manual. Each ligand bridges two Ag+ ions so each silver is tetrahedrally coordinated by four nitrogen atoms. The silver, arsenic and one of the fluorine atoms lie on special positions. Normally the four unique heavy atoms (from Patterson interpretation using SHELXS) would have been refined first isotropically and the remaining atoms found in a difference synthesis, and possibly an intermediate job would have been performed with the heavy atoms anisotropic and the light atoms isotropic. For test purposes we shall simply input the atomic coordinates which assumes isotropic U's of 0.05. In this job all atoms are to be made anisotropic (ANIS). We shall further assume that a previous job has recommended the weighting scheme used here (WGHT) and shown that one reflection is to be suppressed in the refinement because it is clearly erroneous (OMIT). The first 9 instructions (TITL...UNIT) are the same for any SHELXS and SHELXL-93 job for this structure and define the cell dimensions, symmetry and contents. The Siemens SHELXTL program XPREP can be used to generate these instructions automatically for any space group etc. SHELXL-93 knows the scattering factors for the first 94 neutral atoms in the Periodic Table. Ten least-squares cycles are to be performed, and the ACTA instruction ensures that the CIF files 'ags4.cif' and 'ags4.fcf' will be written for archiving and publication purposes. ACTA also sets up the calculation of bond lengths and angles (BOND) and a final difference electron density synthesis (FMAP 2) with peak search (PLAN 20). The HKLF 4 instruction terminates the file and initiates the reading of the 'ags4.hkl' intensity data file. Users migrating from SHELX-76 should note that it is still legal to set up special position constraints on the x,y,z-coordinates, occupation factors, and Uij components (for upwards compatibility). However it is totally unnecessary because the program will do this automatically for any special position in any space group, conventional or otherwise. Similarly the program recognizes polar space groups (P-4 is non-polar) and applies appropriate restraints (H.D. Flack and D. Schwarzenbach, Acta Cryst., A44 (1988) 499-506), so it is no longer necessary to worry about fixing one or more coordinates to prevent the structure drifting along polar axes. It is not necessary to set the overall scale factor using an FVAR instruction for this initial job, because the program will itself estimate a suitable starting value. Comments may be included in the '.ins' file either as REM instructions or as the rest of a line following '!'; this latter facility has been used to annotate this example. TITL AGS4 in P-4 ! title of up to 76 characters CELL 0.71073 8.381 8.381 6.661 90 90 90 ! wavelength and unit-cell ZERR 1 .002 .002 .001 0 0 0 ! Z (formula-units/cell), cell esd's LATT -1 ! non-centrosymmetric primitive lattice SYMM -X, -Y, Z SYMM Y, -X, -Z ! symmetry operators (x,y,z must be left out) SYMM -Y, X, -Z SFAC C AG AS F N S ! define scattering factor numbers UNIT 4 1 1 6 4 8 ! unit cell contents in same order L.S. 10 ! 10 cycles full-matrix least-squares ACTA ! CIF-output, bonds, Fourier, peak search OMIT -2 3 1 ! suppress bad reflection ANIS ! convert all (non-H) atoms to anisotropic WGHT 0.037 0.31 ! weighting scheme AG 2 .000 .000 .000 AS 3 .500 .500 .000 S1 6 .368 .206 .517 ! atom name, SFAC number, x, y, z (usually S2 6 .614 .966 .736 ! followed by sof and U(iso) or Uij); the C 1 .278 .095 .337 ! program automatically generates special N 5 .211 .030 .214 ! position constraints F1 4 .596 .325 -.007 F2 4 .500 .500 .246 HKLF 4 ! read h,k,l,Fo^2,sigma(Fo^2) from 'ags4.hkl' The '.lst' listing file starts with a header followed by an echo of the above '.ins' file. After reading TITL...UNIT the program calculates the cell volume, F(000), absorption coefficient, cell weight and density. If the density is unreasonable, perhaps the unit-cell contents have been given incorrectly. The next items in the '.lst' file are the connectivity table and the symmetry operations used to include a shell of symmetry equivalent atoms (so that all unique bond lengths and angles can be found): ------------------------------------------------------------------------------ Covalent radii and connectivity table for AGS4 in P-4 C 0.770 AG 1.440 AS 1.210 F 0.640 N 0.700 S 1.030 Ag - N N_$4 N_$5 N_$3 As - F2 F2_$6 F1_$7 F1_$6 F1_$1 F1 S1 - C S2_$1 S2 - S2_$2 S1_$1 C - N S1 N - C Ag F1 - As F2 - As Operators for generating equivalent atoms: $1 -x+1, -y+1, z $2 -x+1, -y+2, z $3 -x, -y, z $4 y, -x, -z $5 -y, x, -z $6 y, -x+1, -z $7 -y+1, x, -z ------------------------------------------------------------------------------ Note that in addition to symmetry operations generated by the program, one can also define operations with the EQIV instruction and then refer to the corresponding atoms with _$n in the same way. Thus: EQIV $1 1-x, 1-y, z EQIV $2 x, y-1, z EQIV $3 1-x, -y, z CONF S1 S2_$1 S2_$2 S1_$3 could have been included in 'ags4.ins' to calculate the S-S-S-S torsion angle. Only one new operator would have been required if S2 were bonded to S1 in the original atom list. If EQIV instructions are used, the program renumbers the other symmetry operators accordingly. The next part of the output is concerned with the data reduction: ------------------------------------------------------------------------------ 1475 Reflections read, of which 0 rejected 0 =< h =< 10, -9 =< k =< 10, 0 =< l =< 8, Max. 2-theta = 55.00 0 Systematic absence violations Inconsistent equivalents etc. h k l Fo^2 Sigma(Fo^2) Esd of mean(Fo^2) 3 4 0 387.25 8.54 47.78 1 Inconsistent equivalents 904 Unique reflections, of which 1 suppressed R(int) = 0.0165 R(sigma) = 0.0202 Friedel opposites not merged Maximum memory for data reduction = 955 / 9083 ------------------------------------------------------------------------------ Throughout this documentation, Sigma with a capital S means a summation, and sigma with a small s is an esd. Fo^2 means the EXPERIMENTAL measurement, and so, despite the square, may possibly be slightly negative if the background is higher than the peak as a result of statistical fluctuations etc. R(int) and R(sigma) are defined as follows: R(int) = Sigma | Fo^2 - Fo^2(mean) | / Sigma [ Fo^2 ] where both summations involve all input reflections for which more than one symmetry equivalent is averaged, but not the remaining reflections, and: R(sigma) = Sigma [ sigma(Fo^2) ] / Sigma [ Fo^2 ] over all reflections in the merged list. Since these R-indices are based on F^2, they will tend to be about twice as large as the corresponding indices based on F. The 'esd of the mean' (in the table of inconsistent equivalents) is the rms deviation from the mean divided by the square root of (n-1), where n equivalents are combined for a given reflection. In estimating the sigma(F^2) of a merged reflection, the program uses the value obtained by combining the sigma(F^2) values of the individual contributors, unless the esd of the mean is larger, in which case it is used instead. The memory statistics which appear at various points in the output give the highest elements of the A and B arrays used for the given calculation. Although it is easy to adjust these dimensions, it requires recompiling the program and will rarely be required. For example there is no limit on the number of reflections in this sort/merge stage - if there is less physical memory the program makes more use of the disk, which of course is slower. Special position constraints are then generated and the statistics from the first least-squares cycle are listed (the output has been compacted to fit the page). The maximum vector length refers to the number of reflections processed simultaneously in the rate-determining calculations; usually the program utilizes all available memory to make this as large as possible, subject to a maximum of 511. This maximum may be reduced (but not increased) by means of the fourth parameter on the L.S. (or CGLS) instruction; this may be required to prevent unnecessary disk transfers when large structures are refined on virtual memory systems with limited physical memory. The number of parameters refined in the current cycle is followed by the total number of refinable parameters (here both are 55). ------------------------------------------------------------------------------ Special position constraints for Ag x = 0.0000 y = 0.0000 z = 0.0000 U22 = 1.0 * U11 U23 = 0 U13 = 0 U12 = 0 sof = 0.25000 Special position constraints for As x = 0.5000 y = 0.5000 z = 0.0000 U22 = 1.0 * U11 U23 = 0 U13 = 0 U12 = 0 sof = 0.25000 Special position constraints for F2 x = 0.5000 y = 0.5000 U23 = 0 U13 = 0 sof = 0.50000 Least-squares cycle 1 Maximum vector length =511 Memory required =1095/82388 wR2 = 0.5042 before cycle 1 for 903 data and 55 / 55 parameters GooF = S = 3.480; Restrained GooF = 3.480 for 0 restraints Weight = 1/[sigma^2(Fo^2)+(0.0370*P)^2+0.31*P] where P=(Max(Fo^2,0)+2*Fc^2)/3 ** Shifts scaled down to reduce maximum shift/esd from 17.32 to 15.00 ** N value esd shift/esd parameter 1 2.38015 0.04260 32.401 OSF 2 0.08362 0.00224 14.993 U11 Ag 5 0.02864 0.00580 -3.679 U33 As 11 0.08546 0.00781 4.543 U33 S1 23 -0.01788 0.00444 -4.027 U12 S2 47 0.14422 0.01515 6.218 U33 F1 52 0.13288 0.02330 3.558 U11 F2 Mean shift/esd = 2.053 Maximum = 32.401 for OSF Max. shift = 0.055 A for C Max. dU = 0.049 for F2 ------------------------------------------------------------------------------ Only the largest shift/esd's are printed. More output could have been obtained using 'MORE 2' or 'MORE 3'. The largest correlation matrix elements are printed after the last cycle, in which the mean and maximum shift/esd have been reduced to 0.002 and 0.012 respectively. This is followed by the full table of refined coordinates and Uij's with esd's (too large to include here, but similar to the corresponding table in SHELX-76 except that Ueq and its esd are also printed) and by a final structure factor calculation: ------------------------------------------------------------------------------ Final Structure Factor Calculation for AGS4 in P-4 Total number of l.s. parameters = 55 Maximum vector length = 511 wR2 = 0.0779 before cycle 11 for 903 data and 2 / 55 parameters GooF = S = 1.063; Restrained GooF = 1.063 for 0 restraints Weight = 1/[sigma^2(Fo^2)+(0.0370*P)^2+0.31*P] where P=(Max(Fo^2,0)+2*Fc^2)/3 R1 = 0.0322 for 818 Fo > 4.sigma(Fo) and 0.0370 for all 904 data wR2 = 0.0834, GooF = S = 1.138, Restrained GooF = 1.138 for all data Flack x parameter = 0.0224 with esd 0.0260 (expected values are 0 (within 3 esd's) for correct and +1 for inverted absolute structure) ------------------------------------------------------------------------------ There are some important points to note here. The weighted R-index based on Fo^2 is (for compelling statistical reasons) much higher than the conventional R-index based on Fo with a threshold of say Fo > 4.sigma(Fo). For comparison with structures refined against F the latter is therefore printed as well (as R1). Despite the fact that wR2 and not R1 is the quantity minimized, R1 has the advantage that it is relatively insensitive to the weighting scheme, and so is more difficult to manipulate. Since the structure is non-centrosymmetric, the program has automatically estimated the Flack absolute structure parameter x in the final structure factor summation. In this example x is within one esd of zero, and its esd is also relatively small. This provides strong evidence that the absolute structure has been assigned correctly, so that no further action is required. The program would have printed a warning here if it would have been necessary to 'invert' the structure. For further details see the section on 'absolute structure' below. The two parameters 'refined' ( 2 / 55 ) but not applied in the final structure factor cycle in this case are related to the overall scale and the Flack x parameter; no parameters are 'refined' in the final structure factor cycle for a centrosymmetric structure. This is followed by a list of principal mean square displacements U for all anisotropic atoms. It will be seen that none of the smallest components (in the third column) are in danger of going negative [which would make the atom 'non positive definite' (NPD)] but that the motion of the two unique fluorine atoms is highly anisotropic (not unusual for an AsF6 anion). The program suggests that the fluorine motion is so extended in one direction that it would be possible to represent each of the two fluorine atoms as disordered over two sites, for which x, y and z coordinates are given; this may safely be ignored here (although there may well be some truth in it). The two suggested new positions for each 'split' atom are placed equidistant from the current position along the direction (and reverse direction) corresponding to the largest eigenvalue of the anisotropic displacement tensor. This list is followed by the analysis of variance (reproduced here in squashed form), recommended weighting scheme (to give a flat analysis of variance in terms of Fc^2), and a list of the most disagreeable reflections (which clearly shows that the one reflection suppressed by OMIT is indeed an aberration). For a discussion of the analysis of variance see the second example. ------------------------------------------------------------------------------ Principal mean square atomic displacements U 0.1067 0.1067 0.0561 Ag 0.0577 0.0577 0.0386 As 0.1038 0.0659 0.0440 S1 0.0986 0.0515 0.0391 S2 0.0779 0.0729 0.0391 C 0.1004 0.0852 0.0474 N 0.3029 0.0954 0.0473 F1 may be split into 0.5965 0.3173 0.0288 and 0.5946 0.3324 -0.0369 0.4778 0.1671 0.0457 F2 may be split into 0.5320 0.5089 0.2462 and 0.4680 0.4911 0.2462 Analysis of variance for reflections employed in refinement K = Mean[Fo^2] / Mean[Fc^2] for group Fc/Fc(max) 0.000 0.026 0.039 0.051 0.063 0.082 0.103 0.147 0.202 0.306 1.0 Number in group 94. 89. 90. 91. 89. 91. 89. 91. 88. 91. GooF 1.096 1.101 0.997 1.078 1.187 1.069 1.173 0.922 1.019 0.966 K 1.560 1.053 1.010 1.004 1.007 1.021 1.026 1.002 0.997 0.984 Resolution(A) 0.77 0.81 0.85 0.90 0.95 1.02 1.10 1.22 1.40 1.74 inf Number in group 97. 84. 92. 91. 89. 90. 89. 90. 93. 88. GooF 1.067 0.959 0.935 0.895 1.035 1.040 1.115 1.149 1.161 1.228 K 1.047 1.010 1.009 0.991 1.004 0.996 0.989 1.012 0.997 0.982 R1 0.166 0.100 0.069 0.059 0.051 0.036 0.033 0.027 0.020 0.020 Recommended weighting scheme: WGHT 0.0329 0.3591 Most Disagreeable Reflections (* if suppressed) h k l Fo^2 Fc^2 Delta(F^2)/esd Fc/Fc(max) Resolution(A) * -2 3 1 43.53 7.44 11.14 0.029 2.19 4 4 4 18.32 33.30 3.51 0.062 1.11 -4 1 3 15.79 4.17 3.39 0.022 1.50 0 2 2 41.60 57.32 3.16 0.082 2.61 2 5 0 124.72 100.33 3.06 0.108 1.56 2 3 0 64.43 48.46 3.03 0.075 2.32 -5 4 1 11.04 2.57 2.90 0.017 1.28 2 5 3 42.27 55.48 2.60 0.080 1.27 6 5 2 6.43 1.02 2.56 0.011 1.02 4 6 2 20.16 11.98 2.55 0.037 1.10 6 1 1 55.45 42.28 2.51 0.070 1.35 6 0 5 104.65 126.19 2.49 0.121 0.96 4 1 2 139.30 116.95 2.44 0.117 1.74 9 0 3 39.34 26.06 2.44 0.055 0.86 2 4 4 371.53 327.01 2.36 0.195 1.24 4 3 5 55.69 43.02 2.33 0.071 1.04 -3 6 0 7.51 3.10 2.25 0.019 1.25 -1 4 2 142.05 120.53 2.22 0.119 1.74 0 10 1 2.01 8.31 2.21 0.031 0.83 -2 1 2 1497.02 1361.86 2.20 0.399 2.49 ------------------------------------------------------------------------------ After the table of bond lengths and angles (BOND was implied by the ACTA instruction), the data are merged (again) for the Fourier calculation after correcting for dispersion (because the electron density is real). In contrast to the initial data reduction, Friedel's law is assumed here; the aim is to set up a unique reflection list so that the (difference) electron density can be calculated on an absolute scale. The algorithm for generating the 'asymmetric unit' for the Fourier calculations is general for all space groups, in conventional settings or otherwise. The rms electron density (averaged over all grid points) is printed as well as the maximum and minimum values so that the significance of the latter can be assessed. Since PLAN 20 was assumed, only a peak list is printed (and written to the .res file), followed by a list of shortest distances between peaks (not shown below); PLAN -20 would have produced a more detailed analysis with 'printer plots' of the structure. The last 40 peaks and some of the interatomic distances have been deleted here to save space. In this table, 'distances to nearest atoms' takes symmetry equivalents into account. ------------------------------------------------------------------------------ Bond lengths and angles [severely squashed to fit 80 columns!] Ag - Distance Angles N 2.279(0.006) N_$4 2.279(0.006) 113.08(0.15) N_$5 2.279(0.006) 113.08(0.15) 102.47(0.29) N_$3 2.279(0.006) 102.47(0.29) 113.08(0.16) 113.08(0.15) Ag - N N_$4 N_$5 As - Distance Angles F2 1.640(0.007) F2_$6 1.640(0.007)180.00(0.00) F1_$7 1.672(0.004) 89.08(0.41) 90.92(0.41) F1_$6 1.672(0.004) 89.08(0.41) 90.92(0.41)178.18(0.82) F1_$1 1.672(0.004) 90.92(0.41) 89.08(0.41) 90.01(0.01) 90.01(0.01) F1 1.672(0.004) 90.92(0.41) 89.08(0.41) 90.01(0.01) 90.01(0.01)178.18(0.82) As - F2 F2_$6 F1_$7 F1_$6 F1_$1 S1 - Distance Angles C 1.682(0.007) S2_$1 2.063(0.003) 98.61(0.20) S1 - C S2 - Distance Angles S2_$2 2.011(0.003) S1_$1 2.063(0.003) 105.37(0.07) S2 - S2_$2 C - Distance Angles N 1.147(0.007) S1 1.682(0.007) 175.67(0.49) C - N N - Distance Angles C 1.147(0.007) Ag 2.279(0.006) 152.38(0.45) N - C F1 - Distance Angles As 1.672(0.004) F1 - F2 - Distance Angles As 1.640(0.007) F2 - FMAP and GRID set by program FMAP 2 3 18 GRID -3.333 -2 -1 3.333 2 1 R1 = 0.0370 for 590 unique reflections after merging for Fourier Highest memory used 768 / 6109 Electron density synthesis with coefficients Fo-Fc Maximum = 0.32, Minimum = -0.35 e/A^3, Highest memory used = 768/13827 Mean = 0.00, Rms deviation from mean = 0.07 e/A^3 Fourier peaks appended to .res file x y z sof U Peak Dist to nearest atoms Q1 1 0.0000 0.0000 0.5000 0.25000 0.05 0.32 2.60 N 2.69 C 3.33 AG Q2 1 0.5691 0.3728 0.1623 1.00000 0.05 0.27 1.20 F1 1.34 F2 1.62 AS Q3 1 0.5685 0.3851 -0.1621 1.00000 0.05 0.24 1.19 F1 1.25 F2 1.56 AS Q4 1 0.4075 0.4717 0.2378 1.00000 0.05 0.23 0.81 F2 1.78 AS 1.79 F1 Q5 1 0.5848 0.2667 0.0312 1.00000 0.05 0.23 0.55 F1 2.09 AS 2.47 F1 Q6 1 0.5495 0.3425 -0.1122 1.00000 0.05 0.21 0.83 F1 1.57 AS 1.65 F2 Q7 1 0.2617 -0.1441 0.1446 1.00000 0.05 0.20 1.59 N 2.17 F1 2.40 C Q8 1 0.7221 0.1898 0.0030 1.00000 0.05 0.20 1.55 F1 2.39 N 2.54 N Q9 1 0.1997 0.0293 0.1024 1.00000 0.05 0.19 0.75 N 1.79 C 1.82 AG Q10 1 0.5394 1.0113 0.8165 1.00000 0.05 0.19 0.91 S2 1.41 S2 2.82 S1 ============================================================================== SECOND EXAMPLE (sigi): In the second example (provided as the files 'sigi.ins' and 'sigi.hkl') a small organic structure is refined in the space group P-1. Only the features that are different from the ags4 refinement will be discussed in detail. The structure consists of a five-membered lactone [-C7-C11-C8-C4(O1)-O3-] with a -CH2-OH group [-C5-O2] attached to C7 and a =C(CH3)(NH2) unit [=C9(C10)N6] double-bonded to C8. Of particular interest here is the placing and refinement of the 11 hydrogen atoms via HFIX instructions. The two -CH2- groups (C5 and C11) and one tertiary CH (C7) can be placed geometrically by standard methods; the algorithms have been improved relative to those used in SHELX-76, and the hydrogen atoms are now idealized before each refinement cycle (and after the last). Since N6 is attached to a conjugated system, it is reasonable to assume that the -NH2 group is coplanar with the C8=C9(C10)-N6 unit, which enables these two hydrogens to be placed as ethylenic hydrogens, which requires HFIX (or AFIX) 9n; the program takes into account that they are bonded to nitrogen in setting the default bond lengths. All these hydrogens are to be refined using a 'riding model' (HFIX or AFIX m3) for x, y and z. The -OH and -CH3 groups are trickier, in the latter case because C9 is sp2-hybridized, so the potential barrier to rotation is low and there is no fully staggered conformation available as the obvious choice. Since the data are reasonable, the initial torsion angles for these two groups can be found by means of difference electron density syntheses calculated around the circles which represent the loci of all possible hydrogen atom positions. The torsion angles are then refined during the least-squares refinement. Note that in subsequent cycles (and jobs) these groups will be re-idealized geometrically with RETENTION of the current torsion angle; the circular Fourier calculation is performed only once. Two 'free variables' (2 and 3 - yes, they still exist!) have been assigned to refine common isotropic displacement parameters for the 'rigid' and 'rotating' hydrogens respectively. If these had not been specified, the default action would have been to hold the hydrogen U values at 1.2 times the equivalent isotropic U of the atoms to which they are attached (1.5 for the -OH and methyl groups). The 'sigi.ins' file (which is provided as a test job) is as follows. Note that for instructions with both numerical parameters and atom names such as HFIX and MPLA, is does not matter whether numbers or atoms come first, but the order of the numerical parameters themselves (and in some cases the order of the atoms) is important. ------------------------------------------------------------------------------ TITL SIGI in P-1 CELL 0.71073 6.652 7.758 8.147 73.09 75.99 68.40 ZERR 2 .002 .002 .002 .03 .03 .03 SFAC C H N O UNIT 14 22 2 6 ! no LATT and SYMM needed for space group P-1 L.S. 4 EXTI 0.001 ! refine an isotropic extinction parameter WGHT .060 0.15 ! (suggested by program in last job); WGHT OMIT 2 8 0 ! and OMIT are also based on previous output BOND $H ! include H in bond lengths / angles table CONF ! all torsion angles except involving hydrogen FMAP 2 ! Fo-Fc Fourier PLAN -20 ! printer plots and full analysis of peak list HFIX 147 31 O2 ! initial location of -OH and -CH3 hydrogens from HFIX 137 31 C10 ! circular Fourier, then refine torsion, U(H)=fv(3) HFIX 93 21 N6 ! -NH2 in plane, xyz ride on N, U(H)=fv(2) HFIX 23 21 C5 C11 ! two -CH2- groups, xyz ride on C, U(H)=fv(2) HFIX 13 21 C7 ! tertiary CH, xyz ride on C, U(H)=fv(2) EQIV $1 X-1, Y, Z ! define symmetry operation and tabulate H-bond RTAB H..O H2 O1_$1 ! distance and angle to symmetry equivalent of O1 RTAB XHY O2 H2 O1_$1 ! 'H..O' and 'XHY' are table headings RTAB H..O H6A O1 ! include intramolecular H-bond in tables RTAB XHY N6 H6A O1 EQIV $2 X+1, Y, Z-1 ! include a further intermolecular H-bond in the RTAB H..O H6B O2_$2 ! same tables; involves symmetry equivalent of O2 RTAB XHY N6 H6B O2_$2 ! l.s. planes through 5-ring and through MPLA 5 C7 C11 C8 C4 O3 O1 N6 C9 C10 ! CNC=CCC moiety, then find deviations MPLA 6 C10 N6 C9 C8 C11 C4 O1 O3 C7 ! of last 4 and 3 named atoms resp. too FVAR 1 .06 .07 ! overall scale and free variables for U(H) REM name sfac# x y z sof(+10 to fix it) U11 U22 U33 U23 U13 U12 follow O1 4 0.30280 0.17175 0.68006 11.00000 0.02309 0.04802 = 0.02540 -0.00301 -0.00597 -0.01547 O2 4 -0.56871 0.23631 0.96089 11.00000 0.02632 0.04923 = 0.02191 -0.00958 0.00050 -0.02065 O3 4 -0.02274 0.28312 0.83591 11.00000 0.02678 0.04990 = 0.01752 -0.00941 -0.00047 -0.02109 C4 1 0.10358 0.23458 0.68664 11.00000 0.02228 0.02952 = 0.01954 -0.00265 -0.00173 -0.01474 C5 1 -0.33881 0.18268 0.94464 11.00000 0.02618 0.03480 = 0.01926 -0.00311 -0.00414 -0.01624 N6 3 0.26405 0.17085 0.33925 11.00000 0.03003 0.04232 = 0.02620 -0.01312 0.00048 -0.01086 C7 1 -0.25299 0.33872 0.82228 11.00000 0.02437 0.03111 = 0.01918 -0.00828 -0.00051 -0.01299 C8 1 -0.03073 0.27219 0.55976 11.00000 0.02166 0.02647 = 0.01918 -0.00365 -0.00321 -0.01184 C9 1 0.05119 0.24371 0.39501 11.00000 0.02616 0.02399 = 0.02250 -0.00536 -0.00311 -0.01185 C10 1 -0.10011 0.29447 0.26687 11.00000 0.03877 0.04903 = 0.02076 -0.01022 -0.00611 -0.01800 C11 1 -0.26553 0.36133 0.63125 11.00000 0.02313 0.03520 = 0.01862 -0.00372 -0.00330 -0.01185 HKLF 4 ! read intensity data from 'sigi.hkl'; terminates '.ins' file ------------------------------------------------------------------------------ The data reduction reports 1904 reflections read with -7 >= h >= 7, -8 >= k >= 9 and -9 >= l >= 9. Note that these are the limiting index values; in fact only about 1.5 times the unique volume of reciprocal space was measured. The maximum 2-theta was 50.00, and there were no systematic absence violations, 34 (not seriously) inconsistent equivalents, and 1297 unique data, of which 1 was suppressed (by OMIT). R(int) was 0.0196 and R(sigma) 0.0151. It will be seen that the program uses different default distances to hydrogen for different bonding situations (these may be overridden by the user if desired, of course). These defaults depend on the temperature (set using TEMP) in order to allow for librational effects. The list of default X-H distances is followed by the (squashed) circular difference electron syntheses to determine the C-OH and C-CH3 initial torsion angles: ------------------------------------------------------------------------------ Default effective X-H distances for T = 20.0 C AFIX m = 1 2 3 4 4[N] 3[N] 15[B] 8[O] 9 9[N] 16 d(X-H) = 0.98 0.97 0.96 0.93 0.86 0.89 1.10 0.82 0.93 0.86 0.93 Difference electron density (eA^-3x100) at 15 degree intervals for AFIX 147 group attached to O2. The center of the range is eclipsed (cis) to C7 and rotation is clockwise looking down C5 to O2 -2 0 1 0 0 0 -1 -5 -8 -9 -6 -2 2 5 9 16 29 42 48 39 23 9 0 -2 Difference electron density (eA^-3x100) at 15 degree intervals for AFIX 137 group attached to C10. The center of the range is eclipsed (cis) to N6 and rotation is clockwise looking down C9 to C10 34 37 39 41 38 30 20 15 19 28 39 47 50 43 29 15 12 19 29 35 33 27 25 29 After local symmetry averaging: 21 28 36 41 40 33 24 20 ------------------------------------------------------------------------------ It can be seen that the hydroxyl hydrogen is very clearly defined, but that the methyl group is rotating fairly freely (low potential barrier). After three-fold averaging, however, there is a single difference electron density maximum. The (squashed) least-squares refinement output follows: ------------------------------------------------------------------------------ Least-squares cycle 1 Maximum vector length =511 Memory required =1771/135569 wR2 = 0.1138 before cycle 1 for 1296 data and 105 / 105 parameters GooF = S = 1.134; Restrained GooF = 1.134 for 0 restraints Weight = 1/[sigma^2(Fo^2)+(0.0600*P)^2+0.15*P] where P=(Max(Fo^2,0)+2*Fc^2)/3 N value esd shift/esd parameter 1 0.97914 0.00386 -5.406 OSF 2 0.03486 0.00263 -9.959 FVAR 2 3 0.07515 0.00396 1.048 FVAR 3 4 0.02334 0.00951 2.349 EXTI Mean shift/esd = 0.911 Maximum = -9.959 for FVAR 2 Max. shift = 0.038 A for H10C Max. dU =-0.026 for H5A .......... etc (cycles 2 and 3 omitted) ......... Least-squares cycle 4 Maximum vector length =511 Memory required =1771/135569 wR2 = 0.1044 before cycle 4 for 1296 data and 105 / 105 parameters GooF = S = 1.025; Restrained GooF = 1.025 for 0 restraints Weight = 1/[sigma^2(Fo^2)+(0.0600*P)^2+0.15*P] where P=(Max(Fo^2,0)+2*Fc^2)/3 N value esd shift/esd parameter 1 0.97903 0.00361 -0.001 OSF 2 0.03607 0.00178 0.022 FVAR 2 3 0.07346 0.00379 -0.009 FVAR 3 4 0.02502 0.01089 -0.004 EXTI Mean shift/esd = 0.006 Maximum = -0.182 for tors H10A Max. shift = 0.003 A for H10B Max. dU = 0.000 for H5A Largest correlation matrix elements 0.509 U12 O2 / U22 O2 0.506 U12 O3 / U11 O3 0.508 U12 O2 / U11 O2 0.500 U12 O3 / U22 O3 Idealized hydrogen atom generation before cycle 5 Name x y z AFIX d(X-H) shift Bonded Conformation to determined by H2 -0.6017 0.2095 0.8833 147 0.820 0.000 O2 C5 H2 H5A -0.2721 0.0676 0.9001 23 0.970 0.000 C5 O2 C7 H5B -0.2964 0.1554 1.0576 23 0.970 0.000 C5 O2 C7 H6A 0.3572 0.1389 0.4085 93 0.860 0.000 N6 C9 C8 H6B 0.3073 0.1559 0.2347 93 0.860 0.000 N6 C9 C8 H7 -0.3331 0.4598 0.8575 13 0.980 0.000 C7 O3 C5 C11 H10A -0.2044 0.4191 0.2694 137 0.960 0.000 C10 C9 H10A H10B -0.1761 0.2034 0.2962 137 0.960 0.000 C10 C9 H10A H10C -0.0176 0.2950 0.1525 137 0.960 0.000 C10 C9 H10A H11A -0.3575 0.2948 0.6198 23 0.970 0.000 C11 C8 C7 H11B -0.3198 0.4943 0.5737 23 0.970 0.000 C11 C8 C7 ------------------------------------------------------------------------------ The final structure factor calculation, analysis of variance etc. produces the following edited output: ------------------------------------------------------------------------------ Final Structure Factor Calculation for SIGI in P-1 Total number of l.s. parameters = 105 Maximum vector length = 511 wR2 = 0.1044 before cycle 5 for 1296 data and 0 / 105 parameters GooF = S = 1.025; Restrained GooF = 1.025 for 0 restraints Weight = 1/[sigma^2(Fo^2)+(0.0600*P)^2+0.15*P] where P=(Max(Fo^2,0)+2*Fc^2)/3 R1 = 0.0365 for 1189 Fo > 4.sigma(Fo) and 0.0399 for all 1297 data wR2 = 0.1060, GooF = S = 1.042, Restrained GooF = 1.042 for all data Principal mean square atomic displacements U 0.0504 0.0254 0.0188 O1 0.0491 0.0229 0.0190 O2 0.0513 0.0194 0.0165 O3 0.0326 0.0208 0.0159 C4 0.0375 0.0204 0.0190 C5 0.0440 0.0320 0.0214 N6 0.0329 0.0201 0.0185 C7 0.0276 0.0190 0.0181 C8 0.0288 0.0220 0.0191 C9 0.0494 0.0353 0.0181 C10 0.0353 0.0215 0.0183 C11 Analysis of variance for reflections employed in refinement K = Mean[Fo^2] / Mean[Fc^2] for group Fc/Fc(max) 0.000 0.009 0.017 0.027 0.038 0.049 0.065 0.084 0.110 0.156 1.0 Number in group 135. 125. 130. 139. 119. 133. 130. 128. 131. 126. GooF 1.110 1.006 1.082 1.046 1.093 1.014 0.923 0.996 1.027 0.930 K 1.521 1.121 0.966 1.023 1.008 0.990 0.998 0.998 1.008 1.010 Resolution(A) 0.84 0.88 0.90 0.95 0.99 1.06 1.14 1.25 1.44 1.79 inf Number in group 136. 127. 128. 128. 136. 124. 128. 130. 130. 129. GooF 1.007 0.890 0.865 0.867 0.864 0.921 0.874 1.095 1.256 1.432 K 1.024 1.013 1.017 0.990 0.991 0.989 1.013 0.995 1.037 1.004 R1 0.062 0.049 0.051 0.046 0.034 0.034 0.031 0.039 0.039 0.037 Recommended weighting scheme: WGHT 0.0548 0.1468 ------------------------------------------------------------------------------ The analysis of variance should be examined carefully for indications of systematic errors. If the Goodness of Fit is significantly higher than unity and the scale factor K is appreciably lower than unity in the extreme right columns in terms of both Fc and resolution, then an extinction parameter should be refined (the program prints a warning in such a case). This does not show here because an extinction parameter is already being refined. The scale factor is a little high for the weakest reflections in this example; this may well be a statistical artifact and may be ignored (selecting the groups on Fc will tend to make Fo^2 greater than Fc^2 for this range). The increase in the GooF at low resolution (the 1.79 to infinity range) is caused in part by systematic errors in the model such as the use of scattering factors based on spherical atoms which ignore bonding effects, and is normal for purely light-atom structures (this interpretation is confirmed by the fact that difference electron density peaks are found in the middle of bonds). In extreme cases the lowest or highest resolution ranges can be conveniently suppressed by means of the SHEL instruction; this is normal practice in macromolecular refinements. The weighting scheme suggested by the program is designed to produce a flat analysis of variance in terms of Fc, but makes no attempt to fit the resolution dependence of the Goodness of Fit. It is also written to the end of the .res file, so that it is easy to update it before the next job. In the early stages of refinement it is better to retain the default scheme of WGHT 0.1; the updated parameters should not be incorporated in the next '.ins' file until all atoms have been found and at least the heavier atoms refined anisotropically. The list of most disagreeable reflections and tables of bond lengths and angles (BOND $H - omitted here) and torsion angles (CONF) are followed by the RTAB and MPLA tables: ------------------------------------------------------------------------------ Selected torsion angles -175.08 ( 0.12) C7 - O3 - C4 - O1 5.72 ( 0.15) C7 - O3 - C4 - C8 109.70 ( 0.12) C4 - O3 - C7 - C5 -11.64 ( 0.15) C4 - O3 - C7 - C11 171.12 ( 0.10) O2 - C5 - C7 - O3 -72.04 ( 0.15) O2 - C5 - C7 - C11 -1.47 ( 0.24) O1 - C4 - C8 - C9 177.61 ( 0.12) O3 - C4 - C8 - C9 -176.27 ( 0.14) O1 - C4 - C8 - C11 2.81 ( 0.16) O3 - C4 - C8 - C11 3.09 ( 0.22) C4 - C8 - C9 - N6 176.93 ( 0.13) C11 - C8 - C9 - N6 -177.23 ( 0.13) C4 - C8 - C9 - C10 -3.38 ( 0.22) C11 - C8 - C9 - C10 176.04 ( 0.13) C9 - C8 - C11 - C7 -9.39 ( 0.14) C4 - C8 - C11 - C7 12.36 ( 0.14) O3 - C7 - C11 - C8 -104.74 ( 0.13) C5 - C7 - C11 - C8 Distance H..O 2.041 (0.003) H2 - O1_$1 2.225 (0.002) H6A - O1 2.172 (0.002) H6B - O2_$2 Angle XHY 174.03 (2.37) O2 - H2 - O1_$1 129.29 (0.05) N6 - H6A - O1 155.07 (0.05) N6 - H6B - O2_$2 Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane) 2.344 (0.004) x + 7.411 (0.004) y - 0.015 (0.005) z = 1.978 (0.004) * -0.074 (0.001) C7 * 0.068 (0.001) C11 * -0.042 (0.001) C8 * -0.006 (0.001) C4 * 0.054 (0.001) O3 -0.006 (0.002) O1 -0.098 (0.003) N6 -0.056 (0.002) C9 -0.031 (0.003) C10 Rms deviation of fitted atoms = 0.055 2.544 (0.004) x + 7.349 (0.004) y - 0.166 (0.004) z = 1.863 (0.003) Angle to previous plane (with approximate esd) = 2.45 ( 0.07 ) * 0.005 (0.001) C10 * 0.008 (0.001) N6 * -0.005 (0.001) C9 * -0.034 (0.001) C8 * 0.013 (0.001) C11 * 0.012 (0.001) C4 0.057 (0.002) O1 0.021 (0.002) O3 -0.154 (0.002) C7 Rms deviation of fitted atoms = 0.016 ------------------------------------------------------------------------------ All esd's printed by the program are calculated rigorously from the full covariance matrix, except for the angle between two least-squares planes, which involves some approximations. The contributions to the esds in bond lengths, angles and torsion angles also take the errors in the unit-cell parameters (as input on the ZERR instruction) rigorously into account; an approximate treatment is used to obtain the (rather small) contributions of the cell errors to the esds involving least-squares planes. The free torsional motion of H2 is virtually at right angles to the fairly linear hydrogen bond, so the O-H..O angle has a large esd. On the other hand the 'riding model' constraint applied to the N-H bonds effectively prevents the estimation of a meaningful esd in the two N-H..O angles, hence the unrealistically small values for these two esds. There follows the difference electron density synthesis and line printer 'plot' of the structure and peaks. The highest and lowest features are 0.28 and -0.17 eA^-3 respectively, and the rms difference electron density is 0.04. These values confirm that the treatment of the hydrogen atoms was adequate, and are indeed typical for routine structure analysis of small organic molecules. This output is too voluminous to give here, and indeed users of the Siemens SHELXTL molecular graphics program XP will almost always suppress it by use of the default option of a positive number on the PLAN instruction, and employ interactive graphics instead for analysis of the peak list. ============================================================================== THE REFLECTION DATA FILE 'name.hkl' The '.hkl' file consists of one line per reflection in FORMAT(3I4,2F8.2,I4) for h,k,l,Fo^2,sigma(Fo^2), and batch number. This file should be terminated by a record with all items zero; individual data sets within the file should NOT be separated from one another - the batch numbers serve to distinguish between groups of reflections for which separate scale factors are to be refined (see the BASF instruction). The reflection order and the batch number order is unimportant. This '.hkl' file is read each time the program is run; unlike SHELX-76, there is no facility for intermediate storage of binary data. This enhances computer independence and eliminates several possible sources of confusion. The '.hkl' file is read after the HKLF instruction (which terminates the '.ins' file) has been interpreted. The HKLF instruction specifies the format of the '.hkl' file, and allows scale factors and a reorientation matrix to be applied. For further details see the specification of the HKLF instruction. Lorentz, polarization and absorption corrections are assumed to have been applied to the data in the '.hkl' file. If SHELXA is used for the absorption corrections, it will have read a file name.raw (containing direction cosines) and written 'name.hkl' (without cosines). Since SHELXA can read a SHELXL-93 '.ins' file, empirical absorption corrections (which require SHELXA to calculate Fc) may be applied more than once to the original data in the course of a structure determination simply by running SHELXA immediately before SHELXL-93 with the same '.ins' file. Note that there are special extensions to the '.hkl' format for Laue and powder data, as well as for twinned crystals which cannot be handled by a TWIN instruction alone. In general the '.hkl' file should contain all measured reflections without rejection of systematic absences or merging of equivalents. The systematic absences and R(int) for equivalents provide an excellent check on the space group assignment and consistency of the input data. Since complex scattering factors are used throughout by SHELXL-93 it is important NOT to average Friedel opposites in preparing this file. WHY DOES SHELXL-93 REFINE AGAINST F-SQUARED ? Traditionally most crystal structures have been refined against F. For a well-behaved structure the geometrical parameters and their esd's are almost identical for refinement based on all Fo^2 values and for an old-fashioned refinement against F ignoring data with Fo less than (say) 3.sigma(Fo). For weakly diffracting crystals and in particular for pseudosymmetry problems the refinement against all data is demonstrably superior. The esd's are reduced because more experimental information is used, and the chance of getting stuck in a local minimum is reduced. In addition, the use of a threshold introduces a systematic error which introduces bias into the displacement parameters Uij. On the other hand, it is impossible to refine on F using ALL data, because it would involve taking the square root of a negative number for reflections with negative Fo^2 (i.e. background higher than the peak as a result of statistical fluctuations), and because the estimation of sigma(Fo) from sigma(Fo^2) for small or negative Fo^2 is a difficult statistical problem which requires the assumption of a probability distribution function for the F-values. In the case of pseudosymmetric structures - i.e. the very case where the weak reflections are most important - this distribution function is not known a priori, making it impossible to derive 'correct' sigma(Fo) values and hence correct weights. The diffraction experiment measures intensities and their standard deviations, which after the various corrections give Fo^2 and sigma(Fo^2). If your data reduction program only outputs Fo and sigma(Fo), which as explained above involves serious approximations for weak reflections, you MUST CORRECT YOUR DATA REDUCTION PROGRAM, not simply write a routine to square the Fo values or use HKLF 3 to input Fo and sigma(Fo) to SHELXL-93 (although the latter is legal). Note that if an Fo^2 value is too large to fit format F8.2, then format F8.0 may be used instead - the decimal point overrides the FORTRAN format specification. The use of a threshold for ignoring weak reflections may introduce bias which primarily affects the atomic displacement parameters; it is only justified to speed up the early stages of refinement. In the final refinement ALL DATA should be used except for reflections known to suffer from systematic error (i.e. in the final refinement the OMIT instruction may be used to omit specific reflections - although not without good reason - but not ALL reflections below a given threshold). Anyone planning to ignore this advice should read F. L. Hirshfeld and D. Rabinovich, Acta Cryst., A29 (1973) 510-513 and L. Arnberg, S. Hovmoller and S. Westman, Acta Cryst., A35 (1979) 497-499 first. Refinement against F^2 also facilitates the treatment of twinned and powder data, and the determination of absolute structure. One cosmetic disadvantage of refinement against F^2 is that R-indices based on F^2 are larger than (often about double) those based on F. For comparison with older refinements based on F and an OMIT threshold, a conventional index R1 based on observed F values larger than 4.sigma(Fo) is also printed. The deviation of the Goodness of Fit (S) from unity also tends to be magnified when calculated with F^2. Throughout the output, R indices based on F^2 are denoted R2 and those based on F are denoted R1, e.g. wR2 = [ Sigma[w(Fo^2-Fc^2)^2] / Sigma[w(Fo^2)^2] ]^0.5 R1 = Sigma||Fo|-|Fc|| / Sigma|Fo| For details of the weights w see 'WGHT' below. The Goodness of Fit (S) is always based on F^2: GooF = S = [ Sigma [ w(Fo^2-Fc^2)^2 ] / (n-p) ]^0.5 where n is the number of reflections and p is the total number of parameters refined. In the 'Restrained Goodness of Fit', Sigma[w(yt-y)^2] is added to the numerator and the number of restraints is added to the denominator. This corresponds to treating each restraint as an extra observational equation with weight w = 1/sigma^2. y is the quantity (e.g. a bond length) being restrained and yt is its target value. In these expressions, Sigma is written with a capital S to indicate a summation and a small s for an estimated standard deviation (corresponding to the use of capital and small Greek letters for sigma). In general most statistical quantities are defined as in the I.U.Cr. Commission's report: 'Statistical Descriptors in Crystallography', D. Schwarzenbach et al., Acta Cryst., A45 (1989) 63-75. CIF ARCHIVE FORMAT The CIF format represents a major step forward in the archiving, publication and communication of crystallographic data. At last it is possible to publish crystal structures and incorporate structural data into the crystallographic databases without the expensive and error-prone retyping of tables by hand. CIF format also provides a convenient method of transferring data from one program system to another. The ACTA instruction instructs SHELXL-93 to write two CIF-format files: 'name.fcf' contains the reflection data and 'name.cif' all other data. These files contain all the items needed for archiving the structure; those answers not known to SHELXL-93 (e.g. the color of the crystal) are left as a question mark. In general the final 'name.cif' file should be edited using any text editor to replace most of these question marks. The file is then suitable for deposition in the CSD (organic) and ICSD (inorganic crystal structure) databases. For publication via electronic mail it will normally be necessary to add the authors' names, title, text etc., which may also be done in CIF-format; this is followed by the edited contents of one or more '.cif' files each describing one structure (or possibly the same structure at different temperatures etc.). An example of a paper submitted to Acta Cryst. in this way is provided in Appendix D. At the time of writing it is necessary to send the diagram and Fo/Fc tables by post, though in principle the '.fcf' file is suitable for the direct submission of the Fo/Fc data in CIF-format. SHELXL-93 users are strongly recommended to familiarize themselves with the definitive paper by the I.U.Cr. Commission on Crystallographic Data: S.R. Hall, F.H. Allen and I.D. Brown, Acta Cryst., A47 (1991) 655-685. The auxiliary program CIFTAB is provided with SHELXL-93 to facilitate the transition to CIF. It enables the '.cif' output file from SHELXL-93 to be extended by adding CIF information from other (e.g. diffractometer data processing) programs, and enables a variety of tables to be produced (e.g. crystal data, coordinates, bond lengths and angles, and structure factors) for padding out Ph.D. theses and submission to Journals that have not yet seen the light. Further details of CIFTAB may be found in Appendix C. TREATMENT OF HYDROGEN ATOMS It is difficult to locate hydrogen atoms accurately using X-ray data because of their low scattering power and lack of core electrons, and because the valence electron density is asymmetrical and is not centered at the position of the nucleus (which can be determined by neutron diffraction). In addition hydrogen atoms tend to have larger vibrational and librational amplitudes than other atoms. For many purposes it is preferable to calculate the hydrogen positions according to well-established geometrical criteria and then to adopt a refinement procedure which ensures that a sensible geometry is retained. SHELXL-93 provides a bewildering selection of (AFIX and HFIX) options for positioning and refining hydrogen atoms, as detailed in the section 'atom lists and least-squares constraints'. For routine refinement, however, the riding model is a good choice for tertiary CH (HFIX 13), secondary CH2 (HFIX 23), ethylenic =CH2 (HFIX 93), acetylenic CH (HFIX 163), BH in polyhedral boranes (HFIX 153), and aromatic CH or amide NH (HFIX 43). The hydrogen coordinates are re-idealized before each cycle, and 'ride' on the atoms to which they are attached (i.e. the coordinate shifts are the same for both). In this riding model, the C-H vector remains constant in magnitude and direction, but its origin, i.e. the position of the carbon atom in the unit-cell, may move. Both C and H contribute to the derivative calculations which improves convergence. Alternatively AFIX (or HFIX) 14 etc. performs a similar riding refinement but allows the C-H distance to vary as well (keeping the C-H distances equal within a CH2 or CH3 group). It is possible to use SADI or DFIX to restrain chemically equivalent C-H distances involving different carbons to be equal. Methyl and hydroxyl groups are more difficult to position accurately. If good (low-temperature) data are available the method of choice is HFIX 137 for -CH3 and HFIX 147 for -OH groups; in this approach, a difference electron density synthesis is calculated around the circle which represents the loci of possible hydrogen positions (for a fixed X-H distance and Y-X-H angle). The maximum electron density (in the case of a methyl group after local threefold averaging) is then taken as the starting position for the hydrogen atom(s). In subsequent refinement cycles (and in further least-squares jobs) the hydrogens are re-idealized at the start of each cycle, but the current torsion angle is retained; the torsion angles are allowed to refine whilst keeping the X-H distance and Y-X-H angle fixed. If unusually high quality data are available, AFIX 138 would allow the refinement of a common C-H distance for a methyl group but not allow it to tilt; a variable metric rigid group refinement (AFIX 9 for the carbon followed by AFIX 135 before the first H) would allow it to tilt as well, but still retain tetrahedral H-C-H angles and equal C-H distances within the group. If the data quality is less good, then the refinement of torsion angles may not converge very well. In such cases the hydrogens can be positioned geometrically and refined using a riding model by HFIX 33 for methyl and HFIX 83 for hydroxyl groups. This staggers the methyl groups, and -OH groups attached to saturated carbons, as well as possible; -OH groups attached to aromatic rings are placed in one of the two positions in the plane. In either -OH case the choice of hydrogen position is then determined by best hydrogen bond (to an N, O, Cl or F atom) which can be created. For disordered methyl groups (with two sites rotated by 60 degrees from one another) HFIX 123 is recommended, possibly with refinement of the corresponding site occupation factors via a 'free variable' so that their sum is unity (e.g. 21 and -21). The choice of a suitable (default) O-H distance is very difficult. O-H internuclear distances for isolated molecules in the gas phase are about 0.96 Angstroms (cf. 1.10 for C-H), but the appropriate distance to use for X-ray diffraction must be appreciably shorter to allow for the displacement of the center of gravity of the electron distribution towards the oxygen atom, and also for librational effects. Although the (temperature dependent) value assumed by the program fits reasonably well for O-H groups in predominantly organic molecules, appreciably longer O-H distances are appropriate for low temperature studies of strongly (cooperatively) hydrogen bonded systems - short H..O distances are always associated with long O-H distances. If there are many such O-H groups and good quality data are available, HFIX 88 (or 148) plus SADI restraints to make all the O-H distances approximately equal (with an esd of say 0.01) is a good approach. Hydrogen atoms may also 'ride' on atoms in rigid groups (unlike SHELX-76); for example HFIX 43 could reference carbon atoms in a rigid phenyl ring. In such a case further geometrical restraints (SADI, SAME, DFIX, FLAT) are not permitted on the hydrogen atoms; this is the only exception to the general rule that any number of restraints may be applied to any atom, whatever constraints are also being applied to it. This is much more general than in SHELX-76. If the hydrogen atoms are generated using HFIX, the standard option is to set the isotropic U's to -1.2 (-1.5 for methyl and hydroxyl) which is interpreted as 1.2 (or 1.5) times the equivalent isotropic displacement parameter of the last atom which did not use this facility. A good alternative is to use 'free variables' to constrain the U values of chemically equivalent hydrogens to be equal. Hydrogen atoms are identified as such by their scattering factor numbers, which must correspond to a SFAC name H (or $H). Other elements which need to be specifically identified (e.g. so that HFIX 43 can use different default C-H and N-H distances) are defined similarly. However for the output of the PLAN instruction, hydrogen atoms are identified as those atoms with a radius of less the 0.4 Angstroms (this is not as illogical as it may sound; the PLAN output is concerned with potential hydrogen bonds etc., not with the scattering power of an atom, and SHELXL-93 has to handle neutron as well as X-ray data). OMIT $H (or OMIT_* $H if residues are employed) combined with L.S. 0, FMAP 2 and PLAN -100 enables an 'omit map' to be calculated, which is a convenient way of checking whether there are actually electron density peaks close to the calculated hydrogen positions. In this omit map, the hydrogen atoms are retained but do not contribute to Fc; if a non-zero electron density appears in the 'Peak' column for one of these hydrogens in the Fourier output, then there was an actual peak in the difference electron density synthesis within 0.31 Angstroms of the expected hydrogen position. There are a number of operations in SHELXL-93 in which hydrogen atoms are treated specially, for example in the connectivity array, in atom lists defined using the '>' and '<' symbols, in the atoms following the SAME, ANIS and AFIX instructions, and in the output generated by PLAN. This approach is very convenient for the vast majority of structure refinements. However it may be useful to know how the program decides which atoms are 'hydrogens' in order to be able to treat hydrogens as normal atoms. The program scans the SFAC instructions (either format) for an element named 'H', and if one is found, treats all atoms with this scattering factor number specially. If two or more scattering factors are named 'H', only the last one gets this special treatment, which provides a way of tricking the program into allowing both 'normal' and 'special' hydrogens. Similarly for neutron data, where an SFAC instruction is needed for each element anyway, one could if desired suppress the special treatment of hydrogens by labeling their SFAC instruction 'Hyd' or even 'D'. RESTRAINTS, CONSTRAINTS AND GROUP FITTING, AND DISORDER In crystal structure refinement, there is an important distinction between a 'constraint' and a 'restraint'. A constraint is an exact mathematical condition which enables one or more least-squares variables to be expressed exactly in terms of other variables or constants, and hence eliminated. An example is the fixing of the x, y and z coordinates of an atom on an inversion center. A restraint takes the form of additional information which is not exact but is subject to a probability distribution; for example we could restrain two chemically but not crystallographically equivalent bonds to be approximately equal, with an effective standard deviation of (say) 0.01 Angstroms. A restraint is incorporated in the least-squares refinement as if it were an additional experimental observation; w(yt-y)^2 is added to the quantity Sigma[w(Fo^2-Fc^2)^2] to be minimized, where a quantity y (which is a function of the least-squares parameters) is to be restrained to a target value yt, and the weight w (for either a restraint or a reflection) is 1/sigma^2. In the case of a reflection sigma^2 is estimated using a weighting scheme; for a restraint sigma is simply the effective standard deviation. In SHELXL-93 the restraint weights are multiplied by the square of the Goodness of Fit for the reflection data, which allows for the possibility that the reflection weights may be relative rather than absolute, and also gives the restraints more influence at the early stages of refinement (when the Goodness of Fit is invariably much greater than unity), which improves convergence. Most of the constraints and restraints available in SHELXL-93 have already been widely used in other programs, especially for macromolecular refinement. In SHELXL-93 an effort has been made to make them simple to understand and use, while at the same time avoiding the bias which is introduced when specific target values etc. have to be assumed. For example it is more realistic to assume that a phenyl group is planar and has mm (C2v) symmetry (in both cases within a reasonable tolerance) rather than that it is an exactly regular hexagon with a bond length of 1.39 Angstroms; however both approaches may conveniently be applied using SHELXL-93. The following general categories of constraints and restraints are available using SHELXL-93: 1. Constraints for the coordinates and anisotropic displacement parameters for atoms on special positions: these are generated automatically by the program for ALL special positions in ALL space groups, in conventional settings or otherwise. If the user applies (correct or incorrect) special position constraints using free variables etc., the program assumes this has been done with intent and reports but does not apply the correct constraints. Thus the accidental application of a free variable to a Uij term of an atom on a special position can lead to the refinement 'blowing up' ! 2. Two or more atoms sharing the same site: the xyz and Uij parameters may be equated using the EXYZ and EADP constraints respectively (or by using 'free variables'). The occupation factors may be expressed in terms of a 'free variable' so that their sum is constrained to be constant (e.g. 1.0). If more than two different chemical species share a site, a linear free variable restraint (SUMP) is required to restrain the sum of occupation factors. EADP is also useful for equating the Uij of 'opposite' fluorines of disordered -CF3 groups. 3. Floating origin restraints: these are generated automatically by the program as and when required by the method of H.D. Flack and D. Schwarzenbach, Acta Cryst., A44 (1988) 499-506, so the user should not attempt to fix the origin in such cases by fixing the coordinates of a heavy atom. 4. Geometrical constraints: these include rigid-group refinements (AFIX 6), variable-metric rigid-group refinements (AFIX 9) and various riding models (AFIX/HFIX) for hydrogen atom refinement, for example torsional refinement of a methyl group about the local threefold axis. 5. Fragments of known geometry may be fitted to target atoms (e.g. from a previous Fourier peak search), and the coordinates generated for any missing atoms. Four standard groups are available: regular pentagon, regular hexagon, naphthalene and pentamethylcyclopentadienyl; any other group may be used simply by specifying orthogonal or fractional coordinates in a given cell (AFIX mn with m > 16 and FRAG...FEND). This is usually, but not always, a preliminary to rigid group refinement. 6. Geometrical restraints: a particularly useful restraint is to make chemically but not crystallographically equivalent distances equal (subject to a given or assumed esd) without having to invent a value for this distance (SADI). The SAME instruction can be used to generate such restraints automatically, e.g. when chemically identical molecules or residues are present. This has the same effect as making equivalent bond lengths and angles but not torsion angles equal. The FLAT instruction restrains a group of atoms to lie in a plane (but the plane is free to move and rotate). DFIX and CHIV restrain distances and chiral volumes respectively to target values. When 'free variables' are used for the target values, it is possible to restrain different distances etc. to be equal and to refine their mean value (for which an esd is thus obtained). ALL types of geometrical restraints may involve ANY atom, even if it is part of a rigid group or a symmetry equivalent generated using EQIV $n ... and referenced by _$n, except for hydrogen atoms which ride on rigid group atoms (see preceding section). 7. 'Anti-bumping' restraints may be applied individually, by means of DFIX distance restraints with the distance given as a negative number, or generated automatically by means of the BUMP instruction, which operates on all atoms which have been designated by 'CONN 0' instructions (and so are excluded from the connectivity array). DFIX restraints with negative distance d are ignored if the two atoms are further from one another than |d| in the current refinement cycle; if they are closer than |d|, a restraint is applied to increase the distance to |d| with the given (or assumed) esd. The automatic generation of anti-bumping restraints takes all possible symmetry equivalents into account, and allows a safety margin of 0.5 A so that atoms which move towards one another during the refinement are also covered. In combination with the SWAT instruction for diffuse solvent, BUMP provides a very effective way of handling solvent water in macromolecules. 8. Restraints on anisotropic displacement parameters: three different types of restraint may be applied to Uij values. DELU applies a 'rigid-bond' restraint to Uij of two bonded (or 1,3) atoms; the anisotropic displacement components of the two atoms along the line joining them are restrained to be equal. This restraint was suggested by J.S. Rollett (in Crystallographic Computing, Ed. F.R. Ahmed, S.R. Hall and C.P. Huber, Munksgaard, Copenhagen, (1970) pp. 167-181), and corresponds to the rigid-bond criterion for testing whether anisotropic displacement parameters are physically reasonable (F.L. Hirshfeld, Acta Cryst., A32 (1976) 239-244; K.N. Trueblood and J.D. Dunitz, Acta Cryst., B39 (1983) 120-133). J.J. Didisheim and D. Schwarzenbach (Acta Cryst., A43 (1987) 226-232) have shown that in many but not all cases, rigid- bond restraints are equivalent to the TLS description of rigid body motion in the limit of zero esd's; however this requires that (almost) all atom pairs are restrained in this way, which for molecules with conformational flexibility is unlikely to be appropriate. An extensive study (E. Irmer, Ph.D. Thesis, University of Goettingen, 1990) has shown that this condition is fulfilled within the experimental error for routine X-ray studies of bonds and 1,3-distances between two first-row elements (B to F inclusive), and so may be applied as a 'hard' restraint (low esd). A rigid bond restraint is not suitable for systems with unresolved disorder, e.g. AsF6- anions and dynamic Jahn-Teller effects, although it may be useful in detecting such effects. Isolated (e.g. solvent water) atoms may be restrained to be approximately isotropic, e.g. to prevent them going 'non-positive-definite'; this is a rough approximation and so should be applied as a 'soft' restraint with a large esd (ISOR). Similarly the assumption of 'similar' Uij values for spatially adjacent atoms (SIMU) is useful so that (for example) the thermal ellipsoids increase and change direction gradually going along a side-chain in a polypeptide, but this treatment is approximate and thus also appropriate only for a soft restraint; it is also useful for partially overlapping atoms of disordered groups. A simple way to apply SIMU to all such overlapping atoms is to give a SIMU instruction with no atoms (i.e. all atoms implied) and the third number set to a distance less than the shortest bond, i.e. SIMU 0.02 0.04 0.8 which applies the restraint to all pairs of atoms separated by less than 0.8 Angstroms. Additional SIMU restraints may be included in the same job. SHELXL-93 does not permit DELU, SIMU and ISOR restraints to reference symmetry generated atoms, although this is allowed for all geometrical restraints. To permit such references for displacement parameter restraints as well would considerably complicate the program, and is rarely required in practice. 9. 'Shift limiting restraints' may be applied in SHELXL-93 by the Marquardt algorithm (J. Soc. Ind. Appl. Math., 11 (1963) 431-441). Terms proportional to a 'damping factor' (the first parameter on the DAMP instruction) are added to the least-squares matrix before inversion. Shift limiting restraints are particularly useful in the refinement of structures with a poor data to parameter ratio, and for pseudosymmetric problems. The 'damping factor' should be reduced towards the end of the refinement, otherwise the least-squares estimates of the esd's in the less well determined parameters will be too low (the program does however make a first order correction to the esds for this effect). The shifts are also scaled down if the maximum shift/esd exceeds the second DAMP parameter. In addition, if the actual and target values for a particular restraint differ by more than 100 times the given esd, the program will temporarily increase the esd to limit the influence of this restraint in any one cycle to that produced by a discrepancy of 100 times the esd. This helps to prevent a bad initial model and tight restraints from causing dangerously large shifts in the first cycle. 10. Further constraints may be applied to atom coordinates, occupation and displacement parameters, and to restrained distances (DFIX) and chiral volumes (CHIV), by the use of 'free variables'. Linear combinations of free variables may in turn be restrained (SUMP). Free variables were required for special position constraints and for refining more than one atom on the same site in SHELX-76; their use in this way is allowed (for upwards compatibility) in SHELXL-93, but it is more convenient to use the fully automatic handling of special positions in SHELXL-93, and atoms on multiply occupied sites may be constrained using EXYZ and EADP. For further details see the description of the FVAR instruction. A major advantage of applying chemically reasonable restraints is that a subsequent difference electron density synthesis is often more revealing, because the parameters were not allowed to 'mop up' any residual effects. The refinement of pseudosymmetric structures, where the X-ray data may not be able to determine all of the parameters, is also considerably facilitated, at the cost of making it much easier to refine a structure in a space group of unnecessarily low symmetry! By way of example, assume that the structure contains a cyclopentadienyl (Cp) ring pi-bonded to a metal atom, and that as a result of the high thermal motion of the ring only three of the atoms could be located in a difference electron density map. We wish to fit a regular pentagon (default C-C 1.42 A) in order to place the remaining two atoms, which are input as dummy atoms with zero coordinates. Since the C-C distance is uncertain (there may well be an appreciable librational shortening in such a case) we refine the C5-ring as a 'variable metric' rigid group, i.e. it remains a regular pentagon but the C-C distance is free to vary. In SHELXL-93 this may all be achieved by inserting one instruction (AFIX 59) before the five carbons and one (AFIX 0) after them: AFIX 59 ! AFIX mn with m = 5 to fit pentagon (default C-C C1 1 .6755 .2289 .0763 ! 1.42 A) and n = 9 for v-m rigid-group refinement C2 1 .7004 .2544 .0161 C3 1 0 0 0 ! the coordinates for C3 and C4 are obtained by the C4 1 0 0 0 ! fit of the other 3 atoms to a regular pentagon C5 1 .6788 .1610 .0766 AFIX 0 ! terminates rigid group Since Uij values were not specified, the atoms would refine isotropically starting from U = 0.05. To refine with anisotropic displacement parameters in the same or a subsequent job, the instruction: ANIS C1 > C5 should be inserted anywhere before C1 in the '.ins' file. The SIMU and ISOR restraints on the Uij would be inappropriate for such a group, but: DELU C1 > C5 could be applied if the anisotropic refinement proved unstable. The five hydrogen atoms could be added and refined with the 'riding model' by means of: HFIX 43 C1 > C5 anywhere before C1 in the input file. For good data, in view of possible librational effects, a possible alternative would be: HFIX 44 C1 > C5 SADI 0.02 C1 H1 C2 H2 C3 H3 C4 H4 C5 H5 (which retains a riding model but allows the C-H bond lengths to refine, subject to the restraint that they should be equal within about 0.02 A). In analogous manner it is possible to generate missing atoms and perform rigid group refinements for phenyl rings (AFIX 66) and Cp* groups (AFIX 109). Very often it is possible and desirable to remove the rigid group constraints (by simply deleting the AFIX instructions) in the final stages of refinement; there is good experimental evidence that the ipso-angles of phenyl rings differ systematically from 120 degrees [P.G. Jones, J. Organomet. Chem., 345 (1988) 405; T. Maetzke and D. Seebach, Helv. Chim. Acta, 72 (1989) 624-630; A. Domenicano, Accurate Molecular Structures, eds. Domenicano and Hargittai, Chapter 18, OUP 1992]. As a second example, assume that the structure contains two molecules of poorly defined THF solvent, and that we have managed to identify the oxygen atoms. A rigid pentagon would clearly be inappropriate here, except possibly for placing missing atoms, since THF molecules are not planar. However we can RESTRAIN the 1,2- and the 1,3-distances in the two molecules to be similar by means of a 'similarity restraint' (SAME). Assume that the molecules are numbered O11 C12 ... C15 and O21 C22 ... C25, and that the atoms are given in this order in the atom list. Then we can either insert the instruction: SAME O21 > C25 before the first molecule, or: SAME O11 > C15 before the second. These SAME instructions define a group of five atoms which are considered to be the same as the five (non-hydrogen) atoms which immediately follow the SAME instruction. The entries in the connectivity table for the latter are used to define the 1,2- and 1,3-distances, so the SAME instruction should be inserted before the group with the best geometry. This one SAME instruction restrains five pairs of 1,2- and five pairs of 1,3- distances to be nearly equal, i.e. d(O11-C12) = d(O21-C22), d(C12-C13) = d(C22-C23), d(C13-C14) = d(C23-C24), d(C14-C15) = d(C24-C25), d(C15-O11) = d(C25-O21), d(O11-C13) = d(O21-C23), d(C12-C14) = d(C22-C24), d(C13-C15) = d(C23-C25), d(C14-O11) = d(C24-O21), and d(C15-C12) = d(C25-C22). In addition, it would also be reasonable to restrain the distances on opposite sides of the same ring to be equal. This can be achieved with one further SAME instruction in which we count the other way around the ring. For example we could insert: SAME O11 C15 < C12 before the first ring. The symbol '<' indicates that one must count up the atom list instead of down. The above instruction is exactly equivalent to: SAME O11 C15 C14 C13 C12 This generates 10 further restraints, but two of them [d(C13-C14) = d(C14-C13) and d(C12-C15) = d(C15-C12)] are identities, and each of the others appears twice, so only four are independent and the rest are ignored. It is not necessary to add a similar instruction before the second ring, because the program also automatically generates all 'implied' restraints, i.e. restraints which can be derived by combining two existing distance restraints which refer to the same atom pair. In contrast to other restraint instructions, the SAME instructions must be inserted at the correct positions in the atom list. These similarity restraints provide a very general and powerful way of exploiting non- crystallographic symmetry; in this example two instructions suffice to restrain the THF molecules so that they have (within an assumed standard deviation) twofold symmetry and are the same as each other. However we have not imposed planarity on the rings nor restricted any of the torsion angles. To complicate matters, let us assume that the two molecules are two alternative conformations of a THF molecule disordered on a single site. We must then ensure that the site occupation factors of the two molecules add to unity, and that no spurious bonds linking them are added to the connectivity table. The former is achieved by employing site occupation factors of 21 (i.e. 1 times free-variable 2) for the first molecule and -21 [ 1*(1-fv(2)) ] for the five atoms of the second molecule. Free variable 2 is then the occupation factor of the first molecule; its starting value must be specified on the FVAR instruction. The possibility of spurious bonds is eliminated by inserting 'PART 1' before the first molecule, 'PART 2' before the second, and 'PART 0' after it. Hydrogen atoms can be inserted in the usual way using the HFIX instruction since the connectivity table is 'correct'; they will automatically be assigned the site occupation factors of the atoms to which they are bonded. Finally we would like to refine with anisotropic displacement parameters because the thermal motion of such solvent molecules is certainly not isotropic, but the refinement will be unstable unless we restrain the anisotropic displacement parameters to behave 'reasonably' by means of rigid bond restraints (DELU) and 'similar Uij' restraints (SIMU); fortunately the program can set up these restraints automatically. The DELU restraints restrain the differences in the components of the displacement parameters of two atoms to zero along the 1,2- and 1,3-vector directions, and are derived with the help of the connectivity table. Since the SIMU restraints are much more approximate, we restrict them to atoms which, because of the disorder, are almost overlapping (i.e. are within 0.7 A of each other). Note that the SIMU restraints ignore the connectivity table and are based directly on a distance criterion specifically because this is a sensible way of handling disorder. In order to specify a non-standard distance cutoff which is the third SIMU parameter, we must also give the first two parameters which are the restraint esd's for distances involving non-terminal atoms (0.02) and at least one terminal atom (0.04) respectively. The '.ins' file now contains: HFIX 23 C12 > C15 C22 > C25 ANIS O11 > C25 DELU O11 > C25 SIMU O11 > C25 0.02 0.04 0.7 FVAR ..... 0.75 .... PART 1 SAME O21 > C25 SAME O11 C15 < C12 O11 4 ..... ..... ..... 21 C12 1 ..... ..... ..... 21 C13 1 ..... ..... ..... 21 C14 1 ..... ..... ..... 21 C15 1 ..... ..... ..... 21 PART 2 O21 4 ..... ..... ..... -21 C22 1 ..... ..... ..... -21 C23 1 ..... ..... ..... -21 C24 1 ..... ..... ..... -21 C25 1 ..... ..... ..... -21 PART 0 An alternative type of disorder common for THF molecules and proline residues in proteins is when one atom (say C14) can flip between two positions (i.e. it is the flap of an envelope conformation). If we assign C14 to PART 1, C14' to PART 2, and the remaining ring atoms to PART 0 then the program will be able to generate the correct connectivity, and so we can also generate hydrogen atoms for both disordered components (with AFIX, not HFIX): SIMU C14 C14' ANIS O11 > C14' FVAR ..... 0.7 .... SAME O11 C12 C13 C14' C15 O11 4 ..... ..... ..... C12 1 ..... ..... ..... AFIX 23 H12A 2 ..... ..... ..... H12B 2 ..... ..... ..... AFIX 0 C13 1 ..... ..... ..... PART 1 AFIX 23 H13A 2 ..... ..... ..... 21 H13B 2 ..... ..... ..... 21 PART 2 AFIX 23 H13C 2 ..... ..... ..... -21 H13D 2 ..... ..... ..... -21 AFIX 0 PART 1 C14 1 ..... ..... ..... 21 AFIX 23 H14A 2 ..... ..... ..... 21 H14B 2 ..... ..... ..... 21 AFIX 0 PART 0 C15 1 ..... ..... ..... PART 1 AFIX 23 H15A 2 ..... ..... ..... 21 H15B 2 ..... ..... ..... 21 PART 2 AFIX 23 H15C 2 ..... ..... ..... -21 H15D 2 ..... ..... ..... -21 AFIX 0 C14' 1 ..... ..... ..... -21 AFIX 23 H14C 2 ..... ..... ..... -21 H14D 2 ..... ..... ..... -21 AFIX 0 PART 0 It will be seen that six hydrogens belong to one conformation, six to the other, and two are common. The generation of the idealized hydrogen positions is based on the connectivity table but also takes the PART numbers into account. These procedures should be able to set up the correct hydrogen atoms for all cases of two overlapping disordered groups. In cases of more than two overlapping groups the program will usually still be able to generate the hydrogen atoms correctly by making reasonable assumptions when it finds that an atom is 'bonded' to atoms with different PART numbers, but it is possible that there are examples of very complex disorder which can only be handled by using dummy atoms constrained (EXYZ and EADP) to have the same positional and displacement parameters as atoms with different PART numbers (in practice it may be easier - and quite adequate - to ignore hydrogens except on the two components with the highest occupancies!). When the site symmetry is high, it may be simpler to apply similarity restraints using SADI or DFIX rather than SAME. For example the following three instruction sets would all restrain a perchlorate ion (CL,O1,O2,O3,O4) to be a regular tetrahedron: SAME CL O2 O3 O4 O1 SADI O1 O2 O1 O3 followed immediately by the atoms CL, O1... O4; the SAME restraint makes all the Cl-O bonds equal but introduces only FOUR independent restraints involving the O..O distances, which allows the tetrahedron to distort retaining only one -4 axis, so one further restraint must be added using SADI. or: SADI CL O1 CL O2 CL O3 CL O4 SADI O1 O2 O1 O3 O1 O4 O2 O3 O2 O4 O3 O4 or: DFIX 31 CL O1 CL O2 CL O3 CL O4 DFIX 31.6330 O1 O2 O1 O3 O1 O4 O2 O3 O2 O4 O3 O4 in the case of DFIX, one extra least-squares variable (free variable 3) is needed, but it is the mean Cl-O bond length and refining it directly means that its esd is also obtained directly. If the perchlorate ion lies on a three-fold axis through CL and O1, the SADI method would require the use of symmetry equivalent atoms (EQIV $1 y, z, x and O2_$1 etc. for R3 on rhombohedral axes) so DFIX would be simpler (same DFIX instructions as above with distances involving O3 and O4 deleted) [the number 1.6330 in the above example is of course twice the sine of half the tetrahedral angle]. If you wish to test whether you have understood the full implications of these restraints, try the following problems: (a) A C-O-H group is being refined with AFIX 87 so that the torsion angle about the C-O bond is free. How can we restrain it to make the 'best' hydrogen-bond to a specific Cl- ion, so that the H..Cl distance is minimized and the O-H..Cl angle maximized, using only one restraint instruction (it may be assumed that the initial geometry is reasonably good) ? (b) Restrain a C6 ring to an ideal chair conformation using one SAME and one SADI instruction. Hint: all 1-2, 1-3 and 1-4 distances are respectively equal for a chair conformation, which also includes a regular planar hexagon as a special case. A non-planar boat conformation does not have equal 1-4 distances. To force the ring to be non-planar, the ratio of the 1-2 and 1-3 distances would have to be restrained using DFIX and a free variable. MACROMOLECULES AND OTHER STRUCTURES WITH A POOR DATA/PARAMETER RATIO Macromolecules often contain regions of disordered solvent and do not usually diffract to as high a resolution as small molecules. On the other hand they often contain repeated chemical units which we can exploit by means of similarity restraints to improve the effective data to parameter ratio and hence the precision of the structure. These provide an effective way of incorporating 'non-crystallographic symmetry' into structure refinement. To simplify the application of restraints etc. SHELXL-93 allows a structure to be subdivided into residues, each of which is defined by a residue number and (optionally) a residue class (up to 4 characters). Different residues of the same chemical type may be assigned to the same class and also use identical atom names, but must have different residue numbers. Thus for example the beta carbon atoms in all phenylalanine residues (class PHE) in a polypeptide may all be called 'CB'. Only one instruction would then be needed to add the appropriate idealized hydrogens to all of them and refine them with a 'riding model': HFIX_phe 23 CB To apply 'similarity' distance restraints to all phenylalanines, all that is required is one SAME instruction, which should be inserted before the first atom of the residue with the best geometry (so that its connectivity array may be used to define the 1,2- and 1,3-distances): RESI 23 phe SAME_phe N > CZ [Note: there is of course no restriction on the N 3 ..... ..... ..... order of the atoms in a residue, but it must be ... the same for all residues of the same class] CZ 1 ..... ..... ..... It would also be sensible to apply a planarity restraint to these side chains: FLAT_phe CB > CZ The code '_*' is used to refer to all residues. For example it would be possible to use FLAT in this way to ensure that all peptide carbonyl carbons have planar coordination, but it is easier to do this by restraining their chiral volumes to zero (because the three bonded atoms do not then need to be named explicitly): CHIV_* C 0 assuming that these are the only atoms named 'C'; since the default chiral volume is zero it could be left out. In some cases it is necessary to refer to specific residues, in which case residue numbers should be used. For example the following instruction calculates the torsion angle of a disulfide bridge linking Cys_56 and Cys_124: CONF CB_56 SG_56 SG_124 CB_124 Protein crystallographers will have noticed that SHELXL-93 is fully compatible with the usual protein atom naming conventions, except that all atom names MUST begin with a letter, so the PDB convention of starting some hydrogen atom names with a digit is not allowed; similarly residue classes must begin with a letter and residue numbers must be pure numbers. The auxiliary program PDBINS is provided to generate a SHELXL-93 '.ins' file from a PDB file, incorporating restraints etc. taken from the dictionary file SHELXL.DIC. The general approach to the refinement of large structures with limited reflection data is to proceed GRADUALLY, using all appropriate restraints (and possibly rigid group constraints) in the early stages of refinement, and relaxing them as far as possible only when the refinement has more or less converged. Although full-matrix refinement is normally recommended for small-molecule refinements, it is more efficient in terms of computer resources to use the Konnert-Hendrickson conjugate gradient approach (CGLS) for macromolecular refinement, with judicious insertion of large full-matrix blocks to help to resolve problem areas (e.g. solvent disorder). A final refinement with overlapping full-matrix blocks, possibly restricted to the x, y and z coordinates only, would then be required to obtain the esds in e.g. torsion angles. For a very small protein or polynucleotide with less than 500 non-hydrogen atoms (excluding solvent) a single final xyz-block would suffice. The CGLS refinement is usually very stable; erratic behavior can usually be tracked down to one or more atoms with unreasonably large isotropic or anisotropic displacement parameters, or to refinement of more parameters than the data and restraints can support. If the second number on the L.S. or CGLS instruction is negative (-N) then every Nth reflection is ignored in the least-squares refinement, but is used instead for the calculation of independent R-values when the final structure factor cycle is performed. This enables 'R(free)' to be used to calibrate the sigmas for the various restraints and to check on possible 'over-refinement' (e.g. the refinement of noise peaks from a difference electron density map as solvent atoms). For details see A.T. Brunger, Nature 355 (1992) 472-475. Note the use of the DEFS instruction to change the default sigmas globally! A particularly effective application of R(free) is the decision as to whether the data justify (restrained) anisotropic refinement rather than isotropic. After the structure has more or less reached convergence after isotropic refinement in the usual way, two jobs are run with (for example) 'CGLS 20 -10' so that every 10th reflection is ignored in the refinement but is used instead for calculating R(free). One of the jobs should also contain ANIS (before the first atom), DELU and SIMU (without atom names), and ISOR (for the solvent water, e.g. 'ISOR O1 > LAST'). Only if R(free) is significantly lower for the ANIS job is further anisotropic refinement justified. This is more likely to be the case if the data have been collected to higher resolution (i.e. the data to parameter ratio is higher), but the quality of the data is also important. In general the effective resolution should be better than (very roughly) 1.5 Angstroms for proteins and polynucleotides before anisotropic refinement is justified. It is sensible to apply this R(free) test and - if justified - initiate anisotropic refinement BEFORE attempting to resolve discrete side-chain disorder unless the components of the disorder are well separated spatially, because anisotropic motion can be regarded as an alternative to isotropic motion with discrete disorder for small separations. On the other hand it is a good idea to try to locate as many solvent atoms as possible before applying the test (see below). The similarity restraints on the geometry are unbiased in the sense that no arbitrary numbers in the form of standard bond lengths and angles are required. Thus it should never be necessary to repeat a refinement because more precise values of these quantities are available. If R(free) is used to establish optimal esd's for the restraints, the weights may also be regarded as objective. The only assumption being made is that chemically equivalent bond lengths and angles (i.e. 1,3-distances) are equal in a statistical sense. Similarly the planarity restraints and the restraints on isotropic and anisotropic displacement parameters do not require the use of preconceived (and possibly erroneous) numbers (except zero!). This approach should be used whenever the type of problem (e.g. the extent of the non-crystallographic similarity) and the extent of the data permit. The geometrical similarity approach works very well for 'small-molecule' structures which have become large because there are several chemically identical molecules in the crystallographic asymmetric unit, and well for polynucleotides which may also contain several examples of each repeating unit (especially when divided up into base, furanose and phosphate units). A further advantage of the similarity approach for polynucleotides is that the state of protonation of the bases may be uncertain, making it difficult to know which standard bond lengths etc. to use as target values or in fitting rigid groups; it is safer to assume that the equivalent bases have the same (partial) protonation states, i.e. the 1,2- and 1,3-distances are 'similar' but unknown. On the other hand in proteins some amino-acids may be present many more times (and so will be better refined) than others, and geometric similarity does not help for an amino-acid which is only present once. Thus the recommended approach for proteins and large polypeptides is to use DFIX instructions to restrain 1,2- and 1,3-distances to standard values, with SAME/SADI (and small sigmas) to restrain the components of disordered residues to be similar. FLAT restraints are useful for aromatic residues and (with larger sigmas) for the five atoms involved in each main-chain peptide linkage. It is also very convenient to impose planarity on carbonyl and carboxyl carbons using CHIV (with a chiral volume of zero). All these restraints are set up automatically when the program PDBINS (Appendix B) is used to convert a PDB file for a protein into SHELXL-93 '.ins' format; the restraints are taken from the dictionary file SHELXL.DIC which users are encouraged to extend and adapt to local circumstances. Alternatively a text editor may be used to incorporate the appropriate parts of SHELXL.DIC into the .ins file. Standard (restraint) bond lengths based on the CSD have been tabulated by F.H.Allen, O. Kennard, D.G. Watson, L. Brammer, A.G. Orpen and R. Taylor in Sections 9.5 and 9.6 of Volume C of International Tables for Crystallography (1992), Ed. A.J.C. Wilson, Kluwer Academic Publishers, Dordrecht, pp. 685-791. Suitable parameters for proteins have been given by R.A. Engh and R. Huber, Acta Cryst., A47 (1991) 392-400. For nucleic acids the necessary parameters may be taken from R. Taylor and O. Kennard, J. Mol. Struct., 78 (1982) 1-28 (bases and phosphates) and S. Arnott and D.W.L. Hukins, Biochem. J., 130 (1972) 453-465 (furanose rings). Taylor and Kennard found no evidence that the bases are non-planar, so FLAT can safely be used. With poor resolution data it might be better to fit the bases to the orthogonal coordinates given by R. Taylor and O. Kennard, J. Am. Chem. Soc., 104 (1982) 3209-3212, and then refine them as rigid groups (FRAG...FEND - possibly in an 'include file' - followed by AFIX 176 etc.). It appears that the optimal restraint esds are very nearly independent of the type of structure and the resolution of the data, so normally the default values may be used. These have been established by R(free) and other tests on a variety of structures. The default values may if necessary be reset globally by a DEFS instruction before the individual restraints. The default esds are: all SAME and SADI distances, and DFIX with positive d: 0.03 A (first DEFS parameter); FLAT and CHIV: 0.2 A^3 (second DEFS parameter); DELU: 0.01 A^2 (third DEFS parameter), SIMU: 0.05 (fourth DEFS parameter) if neither atom terminal, otherwise 0.1 (or twice the fourth DEFS parameter); ISOR: 0.1 if atom not bonded to exactly one other atom, otherwise 0.2; DFIX -d (anti- bumping restraints) 0.1 A. The ISOR and DFIX -d defaults are not set by DEFS. Although the above default restraint esds give good results for small molecules and proteins which diffract to 1.2 Angstroms or better, there may be discrepancies involving the rigid bond restraints (indicating that the harmonic model is not such a good approximation, i.e. an ensemble (molecular dynamics) approach may be a better description. In such case DELU and SIMU can be relaxed to about 0.03 and 0.10 respectively for anisotropic refinement, and this model may well give the lowest value for the free R-factor. Some care is needed, because if the restraints are relaxed too far the refinement may become unstable. The refinement may also become unstable (e.g. oscillate rather than converge) if one or more solvent atoms have unreasonably high displacement parameters, in which case they can be deleted. Otherwise either 'DAMP 100' (with L.S.) or 'SLIM .3 .1' (with CGLS) should be tried to damp the refinement (which will then require more cycles for convergence). A further facility primarily intended for macromolecules but also useful for smaller structures is the production of tables using RTAB. When used in conjunction with residues, RTAB provides a convenient way of tabulating standard torsion angles, chiral volumes, and distances and angles involved in (for example) hydrogen bonds. Examples of the latter involving symmetry generated atoms were included in the second test structure (sigi) discussed above. The following instructions would produce sorted tables of the standard protein torsion angles and chiral volumes for the alpha-carbon atoms, assuming that the residues are numbered consecutively (CA_- means the atom CA with the residue number decreased by one): RTAB_* Omeg CA_- C_- N CA RTAB_* Phi C_- N CA C RTAB_* Psi N CA C N_+ RTAB_* Chi N CA CB CG RTAB_* Cvol CA If RTAB_* is not appropriate for a particular residue, e.g. some torsion angles involving the terminal residues, or chi and chiral volume for glycine, the residues in question are simply left out of the tables. The _+ and _- notation may also be used for cyclic peptides by assigning an 'alias' to the first and last residues; for example the residues in a cyclic pentapeptide could be numbered 2 to 6 inclusive, with alias 7 assigned to residue 2 and alias 1 to residue 6, so that all the torsion angles would be tabulated using the above RTAB instructions. The SWAT option introduces one variable and one fixed parameter which enable diffuse solvent to be modeled by Babinet's principle (R. Langridge, D.A. Marvin, W.E. Seeds, H.R. Wilson, C.W. Hooper, M.H.F. Wilkins and L.D. Hamilton, J. Mol. Biol. 2 (1960) 38-64; H. Driessen, M.I.J. Haneef, G.W. Harris, B. Howlin, G. Khan and D.S. Moss, J. Appl. Cryst. 22 (1989) 510-516). This usually produces a significant but not dramatic improvement for the very low order data in macromolecular refinements. One of the most difficult and potentially time-consuming aspects of macromolecular structure refinement is the treatment of solvent water. The relatively diffuse solvent atoms contribute primarily to the lower order reflections and so often constitute a local region in the least-squares parameter space in which there are more parameters than data, i.e. there may be many plausible sets of parameters which fit the data equally well. Thus anisotropic refinement of fully occupied atoms or isotropic refinement of a larger number of water molecules with fractional occupation factors may well fit the data equally well and involve about the same number of parameters in total. The advantage of the former approach is that chemically sensible restraints can be applied to the distances between the waters (and between the solvent and protein atoms). Even when the data only permit an isotropic refinement, it is recommended that the water be refined with full occupancies and 'anti-bumping' restraints until no more waters can be found, and then if necessary (e.g. when there are strong difference Fourier peaks closer than say 2.3 Angstom to waters with relatively high U values) partial occupancies can be assigned. SHELXL-93 enables anti-bumping restraints to be input by hand (DFIX -d) but they will usually be generated automatically by the program (by using the BUMP instruction and flagging the (water) atoms on which it is to operate by 'CONN 0'). The anti-bumping restraints are generated between all water atoms, and between all water and all other atoms, including all possible symmetry equivalents and taking atom types into account (thus potential hydrogen bonds are allowed to be shorter than O..C distances etc.). The following iterative procedure proves effective in practice at building up a network of fully-occupied water molecules, with an acceptable pattern of hydrogen-bonded distances, that is also consistent with the diffraction data. The SWAT and BUMP instructions should be included throughout, with CONN 0 to flag the water molecules and inhibit the generation of accidental bonds (which can for example upset the reidealization of hydrogen atoms each refinement cycle). If the waters are anisotropic 'ISOR 1.0 O1 > LAST' is advisable. After each refinement job, water molecules with (an)isotropic displacement parameters which are too high (e.g. all three principal components greater than 1.2 or 1.4 A^2) should be deleted, and (FMAP 2 / PLAN 200 2.3) difference peaks which make sensible hydrogen bonding distances to water molecules or to other electronegative atoms added; these will not necessarily be the highest peaks. The final table of distances between peaks should be checked to ensure that there are no short distances between the chosen peaks (PLAN 200 2.3 does this automatically). The list of 'disagreeable restraints' after the final refinement cycle in each job should also be checked for short contacts and if necessary one of the offending waters removed. At lower resolution it would be necessary to use a graphical display of the Fo-Fc or 2Fo-Fc electron density to locate the new trial water molecules. This procedure converges after a few jobs when no further water molecules can be eliminated or added. At this point the remaining difference electron density peaks should be inspected carefully to see if it is necessary to add partially occupied discrete solvent atoms in the vicinity of disordered side-chains (if any). An advantage of the full occupancy / antibumping approach is that it prevents water molecules from diffusing into protein regions and thus facilitates remodeling of disordered side-chains etc. In summary, for modeling the solvent the following instructions would be typical: CGLS 10 SWAT 2 2 ! will be updated by the program in the .res file BUMP ! automatic antibumping restraints generated CONN 0 O1 > LAST ! flag water for antibumping and exclude from connectivity ISOR 0.1 O1 > LAST ! for anisotropic waters (ignored for isotropic atoms) FMAP 2 ! Fo-Fc map PLAN 200 2.3 ! difference peaks only written to .res for potential waters and after each job waters would be deleted on editing .res to .ins if bad contacts remain (see final restraints summary) or if U or Ueq have risen to too high a value; selected (or perhaps all) potential waters in the peak-list are then renamed and moved to before the HKLF instruction. It is also possible to monitor progress using the free R factor (CGLS 10 -10). Even if anisotropic refinement is planned, it is a good idea (and it usually makes the eventual R-free test for the anisotropic refinement more favorable) to optimize the water structure in this way first. If this extension of the water is continued after going anisotropic, then an ANIS instruction is needed before the first new water (oxygen) atom. Other useful features for macromolecules include an 'omit map' (OMIT atomnames followed by FMAP), the SHEL instruction for ignoring high and low resolution data, the use of 'include files' for accessing standard fragments or restraint libraries, and provision for synchrotron data at various wavelengths (DISP) as well as Laue data (LAUE plus HKLF 2). The amount of '.lst' file output produced may be reduced substantially by putting 'MORE 0' before the first atom in the '.ins' file, but this facility should only be used when one is sure that the '.ins' file is correct; it might be better to edit (or write a little program to extract information from) the full '.lst' file instead, so that diagnostic information is still available if required. The UNIX 'more' command is useful for browsing through '.lst' files. In contrast to standard macromolecular refinement programs, SHELXL-93 is able to provide reliable estimates of the standard deviations of all refined parameters and of all derived quantities, subject of course to any assumptions implied by the restraints employed (in keeping with the Bayesian philosophy). For example tight geometrical 'similarity restraints' effectively determine mean bond lengths and angles and their esd's, but leave the torsion angles free to refine independently; thus the torsion angles - and their esds - retain their diagnostic value. In summary, a typical refinement of a small protein would take the following course. First the auxiliary program PDBINS would be used to convert the atom coordinates into SHELXL-93 '.ins' format and to extract the necessary restraints from a residue dictionary file (based on 'shelxl.dic' which is provided as a model). This is especially convenient if XPLOR has been used for the structure solution by molecular replacement and/or the initial refinement. Some editing of the '.ins' file may be needed if disorder or non-standard residues are present. Different components of disordered groups should be assigned different 'PART' numbers, and the occupation factors of two components may be refined as p and (1-p) by the use of a free variable (i.e. set to e.g. 21 and -21 in which case a starting value for free variable number 2 should be given as the second parameter on the 'FVAR' instruction). The first SHELXL-93 runs serve to build up a consistent network of fully occupied solvent molecules as explained above. At this point the hydrogen atoms are inserted by removing 'REM ' which precedes the HFIX instructions from PDBINS and the dictionary file. Attachment of hydrogens to more than one component of each disordered group is best performed in a subsequent job by inserting the appropriate AFIX instructions. If the resolution is very good (ca. 1.5 A or better) the R(free) test should now be performed to see whether anisotropic refinement is justified (i.e. two 'CGLS 20 -10' jobs should be run, differing only in that one contains an 'ANIS' instruction). It is a mistake to model discrete disorder (unless the components are very clearly separated), or to include partially occupied solvent, until this test is applied, because anisotropic refinement may well provide an alternative way of modeling these effects. Subsequent anisotropic refinement (if justified) may be combined with improvement of the solvent model and possible modeling of discrete disorder; very often the better phase estimates resulting from the restrained anisotropic refinement give a much clearer difference electron density. Towards the end of this procedure partially occupied solvent may be introduced; where possible the occupation factors should be coupled (using free variables) to those of neighboring disordered side-chains, or an atom may be split into two components with occupancies fixed at 0.5 (i.e. set as 10.5), either as recommended by the program (see the list of principal displacement components) or as deduced from an Fo-Fc Fourier. This maintains the anti-bumping restraints with other solvent and side-chain atoms, but not between disordered components for which the occupancies add up to less than 1.1 (slightly greater than one to allow for hydrogen atom contributions etc.). At various stages in the refinement one of the LIST options can be used to write a phased reflection list to the .fcf file for input into another macromolecular FFT map generating for input into a graphics system. When the refinement has converged, it may be desired to run an xyz-only refinement with overlapping blocks (L.S./BLOC) to obtain esds on the torsion angles and hydrogen bonding distances (the antibumping list may be used to set up tables using RTAB and EQIV - see the sigi test example). Torsion angles and hydrogen-bonding distances are not usually restrained in the refinement, and so their esds have some meaning. Finally 'ACTA 2' and/or WPDB may be used to archive the results. ABSOLUTE STRUCTURE Even if determination of absolute configuration is not one of the aims of the structure determination, it is important to refine ANY non-centrosymmetric structure as the correct 'absolute structure' in order to avoid introducing systematic errors into the bond lengths etc. In some cases the absolute structure will be known with certainty (e.g. proteins), but in others it has to be deduced from the X-ray data. Generally speaking, a single phosphorus or heavier atom suffices to determine an absolute structure using Cu-K(alpha) radiation, and with accurate high-resolution low-temperature data including Friedel opposites such an atom may even suffice for Mo-K(alpha). In the course of the final structure factor calculation the program calculates the Flack absolute structure parameter x and its esd (it is a bonus of the refinement against F^2 that this calculation is a 'hole in one' and doesn't require expensive iteration). A comparison of x with its esd provides an indication as to whether the refined absolute structure is correct or whether it has to be 'inverted' (the program prints a suitable warning should this be necessary). This attempt to refine x 'on the cheap' is reliable when the true value of x is close to zero, but may produce a (possibly severe) underestimate of x for structures which have to be inverted, because x is correlated with positional and other parameters which have not been allowed to vary. Effectively these parameters have adapted themselves to compensate for the wrong (zero) value of x in the course of the refinement, and need to be refined with x to eliminate the effects of correlation. These effects will tend to be greater when the correlation terms are greater, e.g. for pseudo- symmetric structures and for poor data to parameter ratios (say less than 8:1). x can be refined at the same time as all the other parameters using the TWIN and BASF instructions; this implies racemic twinning and so is discussed under TWIN below (see also H.D. Flack, Acta Cryst., (1983) A39, 876-881). For most space groups 'inversion' of the structure simply involves inserting an instruction 'MOVE 1 1 1 -1' before the first atom. Where the space group is one of the 11 enantiomorphous pairs [e.g. P3(1) and P3(2)] the translation parts of the symmetry operators need to be inverted as well to generate the other member of the pair. There are seven cases for which, if the standard setting of the International Tables for Crystallography has been used, inversion in the origin does NOT lead to the inverted absolute structure (in fact, in some cases it leads to a totally different structure: H.D. Flack, personal communication, 1992)! This problem was drawn to the author's attention by D. Rogers in about 1980, but was probably first discussed in print by E. Parthe and L.M. Gelato, Acta Cryst., A40 (1984) 169-183 and by G. Bernardinelli and H.D. Flack, Acta Cryst., A41 (1985) 500-511. The offending space groups and corresponding correct MOVE instructions are: Fdd2 MOVE .25 .25 1 -1 I4(1)cd MOVE 1 .5 1 -1 I4(1) MOVE 1 .5 1 -1 I-42d MOVE 1 .5 .25 -1 I4(1)22 MOVE 1 .5 .25 -1 F4(1)32 MOVE .25 .25 .25 -1 I4(1)md MOVE 1 .5 1 -1 TWINNED CRYSTALS AND REFINEMENT AGAINST POWDER DATA Twinned crystals are refined in SHELXL-93 by the method of Pratt, Coyle and Ibers, J. Chem. Soc. 1971, 2146-2151 (see also Jameson, Acta Cryst., A38 (1982) 817-820). The sum of the Fc^2 values of the individual twin domains, each multiplied by its fractional contribution, is fitted to the observed Fo^2. Since the n fractional contributions must sum to unity, only n-1 of them can be refined independently; the fraction of component 1 is set equal to one minus the sum of the other fractional contributions. Refinement of twinned crystals and refinement against F^2-values derived from powder data are similar in that several reflections with different indices may contribute to a single F^2 observation. For powder data this requires some small adjustments to the format of the '.hkl' file; the batch number becomes the multiplicity m, and where several reflections contribute to the same observation the multiplicity is made positive for the last reflection in the group and negative for the rest. A similar approach is possible for twinned crystals, except that the batch number is replaced by the twin component number, and the batch scale factors (BASF) may be refined to determine the fractional contributions of the components 2, 3, ... k1, the fraction of component 1, is refined as ( 1 - k2 - k3 - ... ). In simple cases, i.e. when the lattices of all components are always coincident, the normal format can be retained in the '.hkl' file, and the index transformation specified with a TWIN instruction. Although SHELXL-93 may be useful for some high symmetry and hence reasonably well resolved powder and fibre diffraction patterns - the various restraints and constraints should be exploited in full to make up for the poor data/parameter ratio - for normal powder data a Rietveld refinement program would be much more appropriate. For both powder (HKLF 6) and twinned data (HKLF 5 or TWIN with HKLF 4), the reflection data are reduced to the 'prime' component, by multiplying Fo^2 and Fc^2 by the ratio Fc^2(prime) / Fc^2(total), before performing the analysis of variance and the Fourier calculations. Similarly 'OMIT h k l' refers to the indices of the prime component. The prime component is the one for which the indices have not been transformed by the TWIN instruction (i.e. m = 1 ), or in the case of HKLF 5 or HKLF 6 the component given with positive m (i.e. the last contributor to a given intensity measurement, not necessarily with |m| = 1). For powder data the least-squares refinement fits the overall scale factor (osf^2 where osf is given on the FVAR instruction) times the multiplicity weighted sum of calculated intensities to Fo^2: (Fc^2)* = osf^2 [ m(1) * Fc(1)^2 + m(2) * Fc(2)^2 + m(3) * Fc(3)^2 + ... ] where the multiplicities of the contributors are given in the place of the batch numbers in the '.hkl' file. Since it is then not possible to define batch numbers as well, 'BASF' cannot be used with powder data. For twinned data (TWIN or HKLF 5) the expression becomes: (Fc^2)* = osf^2 [ k(1) * Fc(1)^2 + k(2) * Fc(2)^2 + k(3) * Fc(3)^2 + ... ] where the starting values for the k(2), k(3), ... are given on the BASF instruction, and k(1) is defined such that Sigma[k(m)] = 1. If no BASF instruction is used, all the k(m) are made equal. m is the component number given in the place of the batch number in the '.hkl' file; if TWIN is used to generate the components, m is 1 for the initial indices, 2 after applying the TWIN matrix once, 3 after applying it twice, etc. The parameter ncomp must be given on the TWIN instruction if the matrix is to be applied more than once. The following cases are relatively common: (a) The lower symmetry trigonal, tetragonal, hexagonal or cubic Laue groups may be twinned so that they look (more) like the corresponding higher symmetry Laue groups (assuming c unique except for cubic): TWIN 0 1 0 1 0 0 0 0 -1 plus one BASF parameter if the twin components are not equal in scattering power. (b) Orthorhombic with a and b approximately equal may emulate tetragonal: TWIN 0 1 0 1 0 0 0 0 -1 plus one BASF parameter for unequal components. (c) Monoclinic with beta approximately 90 degrees may emulate orthorhombic: TWIN 1 0 0 0 -1 0 0 0 -1 plus one BASF parameter for unequal components. (d) Monoclinic with a and c approximately equal and beta approximately 120 degrees may emulate hexagonal [P2(1)/c would give absences and possibly also intensity statistics corresponding to P6(3)]. There are three components, so ncomp must be specified and the matrix is applied once to generate the indices of the second component and twice for the third component. In German this is called a 'Drilling' as opposed to a 'Zwilling' (with two components): TWIN 0 0 1 0 1 0 -1 0 -1 3 plus TWO BASF parameters for unequal components. If the data were collected using an hexagonal cell, then an HKLF matrix would also be required to transform them to a setting with b unique: HKLF 4 1 1 0 0 0 0 1 0 -1 0 (e) Refinement of racemic twinning may be performed by adding the following two instructions to the '.ins' file (and retaining HKLF 4): TWIN BASF 0.5 since the default TWIN matrix inverts the indices. In this example, the BASF coefficient is the Flack absolute structure parameter x (H.D. Flack, Acta Cryst., (1983) A39, 876-881; G. Bernardinelli and H.D. Flack, Acta Cryst., A41 (1985) 500-511). Refinement of racemic twinning should normally only be attempted after all non-hydrogen atoms have been located AND the program suggests that it would be advisable. If racemic twinning is refined in this way, the automatic calculation of the Flack x parameter in the final structure factor cycle is suppressed, since the BASF parameter is x. If general and racemic twinning are to be refined simultaneously, ncomp should be doubled and given a negative sign, and there should be |ncomp|-1 BASF twin component factors (or none, in the unlikely event that all are to be fixed as equal). The inverted components follow those generated using the TWIN matrix, in the same order. In such a case a single Flack x parameter is no longer appropriate; the program will still estimate a value, which should be zero since the effect has already been taken into account, but its esd gives a guide to the reliability of the racemic refinement. The HKLF 5 and 6 instructions force MERG 0, i.e. neither a transformation of reflection indices into a standard form nor a sort-merge is performed. If twinning is specified using the TWIN instruction, any MERG instruction may be used and the default remains MERG 2. Although this is always safe for racemic twinning, there may be other forms of twinning for which it is not permissible to sort-merge first. Whether or not MERG is used, the program ignores all systematically absent contributions, with the result that a reflection is excluded from the data if it is systematically absent for all components. Twinning usually arises for good structural reasons. When the heavy atom positions correspond to a higher symmetry space group it may be difficult or impossible to distinguish between twinning and disorder (of the light atoms); see W. Hoenle and H.G. von Schnering, Z. Krist., 184 (1988) 301-305. Since refinement as a twin usually requires only two extra instructions and one extra parameter, in such cases it should be attempted first, before investing many hours in a detailed interpretation of the 'disorder'! THE '.ins' INSTRUCTION FILE - DETAILED SPECIFICATION The rest of this documentation should be regarded as a reference manual rather than light reading! Defaults are given in square brackets in this documentation; '#' indicates that the program will generate a suitable default value based on the rest of the available information. Continuation lines are flagged by '=' at the end of a line, the instruction being continued on the next line which must start with four spaces. Other lines beginning with four spaces are treated as comments, so blank lines may be added to improve readability. All characters following '!' or '=' in an instruction line are ignored, except after TITL, SYMM or EQIV (for which continuation lines are not allowed). The '.ins' file may include an instruction of the form: +filename (the '+' character MUST be in column 1). This causes further input to be taken from the named file until an 'END' instruction is encountered in that file, whereupon the file is closed and instructions are taken from the next line of the '.ins' file. The input instructions from such an 'include' file are not echoed to the '.lst' and '.res' file, and may NOT contain FVAR, BASF, EXTI or SWAT instructions or atoms (except inside a FRAG...FEND section) since this would prevent the '.res' file from being used unchanged for the next refinement job (after renaming as '.ins'). The '+filename' facility enables standard fragment coordinates or long lists of restraints etc. to be read from the same files for each refinement job, and for different structures to access the same fragment or restraint files. One could also for example store the LATT and SYMM instructions for different space groups, or neutron scattering factors for particular elements, or LAUE instructions followed by wavelength-dependent scattering factors, in suitably named files. Since these 'include' files are not echoed, it is a good idea to test them as part of an '.ins' file first, to check for possible syntax errors. Such 'include' files may be nested; the maximum allowed depth depends upon the operating system and compiler used. Note that on some (e.g. IBM mainframe) computers, 'filename' is a dummy name (DDNAME) which must be defined in the JCL or REXX macro used to submit the job. TITL [ ] Title of up to 76 characters, to appear at suitable places in the output. The characters '!' and '=', if present, are part of the title rather than having a special significance. CELL lambda a b c alpha beta gamma Wavelength and unit-cell dimensions in Angstroms and degrees. ZERR Z esd(a) esd(b) esd(c) esd(alpha) esd(beta) esd(gamma) Z value (number of formula units per cell) followed by the estimated standard deviations in the unit-cell dimensions. LATT N [1] Lattice type: 1=P, 2=I, 3=rhombohedral obverse on hexagonal axes, 4=F, 5=A, 6=B, 7=C. N must be made negative if the structure is non-centrosymmetric. SYMM symmetry operation Symmetry operators, i.e. coordinates of the general positions as given in International Tables. The operator x, y, z is always assumed, so MUST NOT be input. If the structure is centrosymmetric, the origin MUST lie on a center of symmetry. Lattice centering should be indicated by LATT, not SYMM. The symmetry operators may be specified using decimal or fractional numbers, e.g. 0.5-x, 0.5+y, -z or Y-X, -X, Z+1/6; the three components are separated by commas. SFAC elements Element symbols which define the order of scattering factors to be employed by the program. The first 94 elements of the periodic system are recognized. The element name may be preceded by '$' but this is not obligatory (the '$' character is allowed for logical consistency but is ignored). The program uses the neutral atom scattering factors, f' and f" and absorption coefficients from International Tables for Crystallography, Volume C (1992), Ed. A.J.C. Wilson, Kluwer Academic Publishers, Dordrecht: Tables 6.1.1.4 (pp. 500-502), 4.2.6.8 (pp. 219-222) and 4.2.4.2 (pp. 193-199) respectively. The covalent radii stored in the program are based on experience rather than taken from a specific source, and are deliberately overestimated for elements which tend to have variable coordination numbers so that 'bonds' are not missed, at the cost of generating the occasional 'non-bond'. The default radii (not those set for individual atoms by CONN) are printed before the connectivity table. SFAC label a1 b1 a2 b2 a3 b3 a4 b4 c f' f" mu r wt Scattering factor in the form of an exponential series, followed by real and imaginary dispersion terms, linear absorption coefficient, covalent radius and atomic weight. Except for the 'label' and atomic weight the format is the same as that used in SHELX-76. label consists of up to 4 characters beginning with a letter (e.g. Ca2+) and should be included before a1; the first label character may be a '$', but this would be ignored (note however that the '$', if used, counts as one of the four characters). The two SFAC formats may be used in the same '.ins' file; the order of the SFAC instructions (and the order of element names in the first type of SFAC instruction) define the scattering factor numbers which are referenced by atom instructions. The units of mu should be barns/atom, as in Table 4.2.4.2 of International Tables, Volume C (see above). DISP E f' f" [#] mu [#] The DISP instruction allows the dispersion and (optionally) the absorption coefficient of a particular element E (the name may be optionally prefaced by '$') to be read in without having to use the full form of the SFAC instruction. It will typically be used for synchrotron data where the wavelength does not correspond to the values (for Cu, Mo and Ag radiation) for which these terms are stored in the program. All other terms on the SFAC instruction are independent of the wavelength, so its short form may then be used. DISP instructions, if present, MUST come between SFAC and UNIT. UNIT n1 n2 ... Number of atoms of each type in the unit-cell, in SFAC order. LAUE E Wavelength-dependent values of f' and f" may be defined for an element E by means of the LAUE instruction, which is used in conjunction with the HKLF 2 reflection data format (in which the wavelength is given separately for each reflection). This is primarily intended for refinement of structures against Laue data collected using synchrotron radiation, but could also be used for refinement of a structure using data collected at different wavelengths employing other sources. There is no provision for handling overlapping reflection orders. Scaling for the source intensity distribution and Lp, absorption corrections etc. must have been performed before using SHELXL-93. A dummy wavelength of say 0.7 Angstrom should be given on the CELL instruction, and the absorption coefficient estimated by the program should be ignored. The element symbol may be preceded by '$' but this is optional; it must be followed by at least one blank or the end of the line. Any remaining information on the LAUE instruction line is ignored. The line immediately following the LAUE instruction is always ignored, and so may be used for headings. The following lines contain values of wavelength (in Angstroms), f' and f" in FORMAT(F7.3,2F8.3); further information (e.g. mu) may follow on the same line but will be ignored. The wavelength values must be in ascending order and will be linearly interpolated; the wavelength intervals do not need to be equal (but it is more efficient if most of them are) and should indeed be smaller in the region of an absorption edge. This list is terminated by a record in which all three values are given as zero. There should only be one LAUE instruction for each element type; if a reflection wavelength is outside the range specified, the constant f' and f" values defined by the corresponding SFAC instruction are used instead. A LAUE instruction must be preceded by (normal) SFAC and UNIT instructions referencing the elements in question, and by all atoms. Thus the LAUE instruction(s) are usually the last instructions before HKLF 2 (or -2) at the end of the '.ins' file (which facilitates editing). The +filename construction may conveniently be used to read long LAUE tables from 'include' files without echoing them. If computer memory is restricted (e.g. in the real-mode PC version of SHELXL-93) then the LAUE tables should not cover a larger range than is strictly necessary for the reflection data employed. REM Followed by a comment on the same line. This comment is copied to the results file ('.res'). A line beginning with at least one blank may also be used as a comment, but such comments are only copied to the .res file if the line is completely blank; REM comments are always copied. Comments may also be included on the same line as any instruction following the character '!', and are copied to the .res file (except in the case of atoms and FVAR, EXTI, SWAT and BASF instructions). MORE m [1] MORE sets the amount of (printer) output; m takes a value in the range 0 (least) to 3 (most verbose). MORE 0 also suppresses the echoing to the '.lst' file of any instructions or atoms which follow it (until the next MORE instruction). TIME t [#] If the time t (measured in seconds from the start of the job) is exceeded, SHELXL-93 performs no further least-squares cycles, but goes on to the final structure factor calculation followed by bond lengths, Fourier calculations etc. The default value of t is installation dependent, and is either set to 'infinity' or to a little less than the maximum time allocation for a particular class of job. Usually t is 'CPU time', but on some simpler computer systems (e.g. PC's) the elapsed time may have to be used instead. END END is used to terminate an 'include' file, and may also be included after HKLF in the '.ins' file (for compatibility with SHELX-76). REFLECTION DATA INPUT AND MASSAGING Before running SHELXL-93, a reflection data file 'name.hkl' must have been prepared. The HKLF command tells the program which format has been chosen for this file, and allows the indices to be transformed using the 3x3 matrix r11...r33, so that the new h is r11*h + r12*k + r13*l etc. The program will not accept matrices with negative or zero determinants. It is essential that the cell, symmetry and atom coordinates in the '.ins' file correspond to the indices AFTER transformation using this matrix. HKLF n [0] s [1] r11...r33 [1 0 0 0 1 0 0 0 1] wt [1] m [0] n is negative if reflection data follow, otherwise they are read from the '.hkl' file. The data are read in FORMAT(3I4,2F8.2,I4) (except for |n| < 3) subject to FORTRAN-77 conventions. The data are terminated by a record with h, k and l all zero (except |n| = 1, which contains a terminator and a checksum). In the reflection formats given below, BN stands for batch number. If BN is greater than one, Fc^2 is multiplied by the (BN-1)'th coefficient specified by means of BASF instructions (see below). If BN is zero or absent, it is reset to one. The multiplicative scale s multiplies both Fo^2 and sigma(Fo^2) (or Fo and sigma(Fo) for n = 1 or 3). The multiplicative weight wt multiplies all 1/sigma^2 values and m is an integer 'offset' needed to read 'condensed data' (HKLF 1); both are included for compatibility with SHELX-76. Negative n is also only retained for upwards compatibility; it is much better to keep the reflection data in the 'name.hkl' file, otherwise the data can easily get lost when editing 'name.res' to 'name.ins' for the next job. n = 1: SHELX-76 condensed data (BN is set to one). 'Condensed data' impose unnecessary index restrictions and can introduce rounding errors; although they still have their uses (email!), SHELXL-93 cannot generate condensed data and their use is discouraged. n = 2: h k l Fo^2 sigma(Fo^2) BN [1] lambda [#] in FORMAT(3I4,2F8.2,I4,F8.4) for refinement based on singlet reflections from Laue photographs. The data are assumed to be scaled for source intensity distribution and geometric factors and (if necessary) corrected for absorption. If lambda is zero or absent the value from the CELL instruction is used. n = 2 switches off the merging of equivalent reflections BEFORE l.s. refinement (i.e. sets MERG 0); equivalents and measurements of the same reflections at different wavelengths are merged after least-squares refinement and the subsequent application of a dispersion correction, but before Fourier calculations. The remaining options (n > 2) all require FORMAT(3I4,2F8.2,I4); as is normal for a FORTRAN program, other formats (e.g. F8.0) may be used for the floating point numbers provided that eight columns are used in all and a decimal point is present. n = 3: h k l Fo sigma(Fo) BN [1] (if BN is absent or zero it is set to 1). The use of data corresponding to this format is NOT RECOMMENDED, since the generation of Fo and sigma(Fo) from Fo^2 and sigma(Fo^2) is a tricky statistical problem and could introduce bias. n = 4: h k l Fo^2 sigma(Fo^2) BN [1] for the standard reflection data file. Since Fo^2 is obtained as the difference of the experimental peak and background counts, it may be positive or (occasionally) negative. n = 5: h k l Fo^2 sigma(Fo^2) m where m is the twin component number. Each measured Fo^2 value is fitted to the sum of k[|m|]*Fc[|m|]^2 over all contributing components, multiplied by the overall scale factor. m should be given as positive for the last contributing component and negative for the remaining ones (if any). The values of Fo^2 and sigma(Fo^2) are taken from the last ('prime') reflection in a group, and may simply be set equal for each component, but the indices h,k,l will in general take on different values for each component. The starting values of the twin factors k[2]..k[max(m)] are specified on BASF instruction(s); k[1] is given by one minus the sum of the other twin factors. Note that many simple forms of twinning can also be handled with HKLF 4 and a TWIN instruction to generate the indices of the remaining twin component(s); HKLF 5 is required if the reciprocal space lattices of the components cannot be superimposed exactly. HKLF 5 sets MERG 0. n = 6: h k l Fo^2 sigma(Fo^2) m as for n = 5, there may be one or more sets of reflection indices corresponding to a single Fo^2 value. The last reflection in a group has a positive m value and the previous members of the group have negative m. The values of Fo^2 and sigma(Fo^2) are taken from the last ('prime') reflection in a group, and may simply be set to the same values for the others. m is here the reflection MULTIPLICITY, and is defined as the number of equivalent permutations of the given h, k and l values, not counting Friedel opposites. This is intended for fitting resolved powder data for high symmetry crystal systems. For example, in a powder diagram of a crystal in the higher cubic Laue class (m3m) the reflections 3 0 0 (with multiplicity 3) and 2 2 1 (multiplicity 12) would contribute to the same measured Fo^2. HKLF 6 sets MERG 0. HKLF 6 may not be used with BASF. THERE MAY ONLY BE ONE HKLF INSTRUCTION AND IT MUST COME LAST, except when HKLF -n is followed by reflection data in the '.ins' file, in which case the file is terminated by the end of the reflection data. Negative n is retained for compatibility with SHELX-76 but is not recommended! OMIT s [-3] 2-theta(lim) [180] s is a threshold for flagging reflections as 'unobserved'. Note that if no OMIT instruction is given, ALL reflections except those with large negative Fo^2 [i.e. Fo^2 < -3.sigma(Fo^2)] are treated as 'observed'. Unobserved data are not used for least-squares refinement or Fourier calculations, but are retained for the calculation of R-indices based on all data, and may also appear (flagged with an asterisk) in the list of reflections for which Fo^2 and Fc^2 disagree significantly. Internally in the program s is halved and applied to Fo^2, so for positive Fo^2 the test is roughly equivalent to suppressing all reflections with Fo < s * sigma(Fo), as required for consistency with SHELX-76. Note that s may be set to 0 (to suppress reflections with negative Fo^2) or (as in the default setting) to a negative threshold (to suppress very negative Fo^2) which has no equivalent in SHELX-76. An OMIT instruction with a positive s value is NOT ALLOWED in combination with ACTA, because it may introduce a bias in the final refined parameters; individual aberrant reflections may still be suppressed using OMIT h k l, even when ACTA is used. 2-theta(lim) defines a limiting 2-theta above which reflections are totally ignored; they are rejected immediately on reading in. This facility may be used to save computer time in the early stages of structure refinement, and is also sometimes useful for macromolecules, but should not be used without very good reason! The SHEL command may be used to flag reflections as 'unobserved' (but retain them in the data set) above or below particular 2-theta limits. OMIT followed by atom names but no numbers may be used to calculate an 'omit map' and is described in the section 'Atom Lists ...'. OMIT h k l The reflection h k l is flagged as 'unobserved' in the list of merged reflections after data reduction. Since there may be perfectly justified reasons for ignoring individual reflections (e.g. when a reflection is truncated by the beam stop) this form of OMIT is allowed with ACTA; however it should not be used indiscriminately. OMIT takes effect after MERG, so if the default MERG 2 is used, OMIT must refer to the indices in the final reflection list, not necessarily as input. It will always be safe to use the indices as given in the list of reflections which do not agree well that is printed after least-squares refinement; however if no sort-merge is performed, OMIT suppresses all reflections with matching indices. SHEL lowres [infinite] highres [0] Reflections outside the specified resolution range in Angstroms are flagged as 'unobserved' in the list of merged reflections after data reduction. This instruction may be useful for macromolecules. BASF scale factors Relative batch scale factors are included in the least-squares refinement based on the batch numbers in the '.hkl' file. For batch number BN, the Fc^2 value is multiplied by the (BN-1)'th scale factor from the BASF instruction, as well as by the overall scale factor. For batch number one (or zero), Fc is multiplied by the overall scale factor, but not by a batch scale factor. The least-squares matrix will be singular if there are no reflections with BN=1 (or zero), so the program considers this to be an error. Note that BASF scale factors, unlike the overall scale factor (see FVAR) are relative to F^2, not F. For twinned crystals, i.e. when either TWIN or HKLF 5 are employed, BASF specifies the fractional contributions of the various twin components. TWIN 3x3 matrix [-1 0 0 0 -1 0 0 0 -1] ncomp [2] ncomp is the number of twin components (2 or greater) and the matrix is applied (iteratively if |ncomp| > 2) to generate the indices of the twin components from the input reflection indices, which apply to the first (prime) component. If a transformation matrix is also given on the HKLF instruction, it is applied first before the (iterative) application of the TWIN matrix. This method of defining twinning allows the standard HKLF 4 format to be used for the '.hkl' file, but can only be used when the reciprocal lattices for all twinned components are metrically superimposable. In other cases HKLF 5 format must be used. The Fo^2 values are fitted to the sum of k[m]*Fc[m]^2 multiplied by the overall scale factor, where k[1] is one minus the sum of k[2], k[3], .. and the starting values for the remaining twin fractions k[2], k[3], .. are specified on a BASF instruction. Only ONE TWIN instruction is allowed. If BASF is omitted the TWIN factors are all assumed to be equal (i.e. 'perfect' twinning). For example, if a structure in the space group P2(1)/c with a and c almost equal and beta close to 120 degrees is pseudohexagonally twinned so that the space group appears to be P6(3) (with the pseudo-6(3) axis along b), refinement could be performed with the instructions: TWIN 0 0 1 0 1 0 -1 0 -1 3 BASF .35 .25 The CELL, LATT and SYMM instructions would give the true monoclinic cell (in the conventional setting with the 2(1) axis along b). A full set of monoclinic data would be prerequisite for a satisfactory refinement. If the twinning is 'perfect', the BASF instruction would be left out, and a unique hexagonal set of data should suffice. If the data had been collected on a hexagonal cell in this example, an HKLF conversion matrix would be needed as well to make b the 2(1) axis first, e.g.: HKLF 4 1 1 0 0 0 0 1 0 -1 0 Refinement of racemic twinning may be performed with: TWIN -1 0 0 0 -1 0 0 0 -1 2 (or just TWIN, since these are the defaults) BASF 0.4 so that the BASF coefficient is the Flack absolute structure parameter x (H.D. Flack, Acta Cryst., (1983) A39, 876-881; G. Bernardinelli and H.D. Flack, Acta Cryst., A41 (1985) 500-511). In this case the program does not calculate a separate Flack parameter in the final structure factor calculation, but uses the BASF parameter and its esd for the Flack parameter in the '.cif' output. If the racemic twinning is present at the same time as normal twinning, ncomp should be doubled (because there are twice as many components as before) and given a negative sign (to indicate to the program that the inversion operator is to be applied multiplicatively with the specified TWIN matrix). The number of BASF parameters, if any, should be increased from m-1 to 2m-1 where m is the original number of components (equal to the new |ncomp| divided by 2). The TWIN matrix is applied m-1 times to generate components 2 ... m from the prime reflection (component 1); components m+1 ... 2m are then generated as the Friedel opposites of components 1 ... m. In such a case the program will estimate a Flack parameter in the final structure factor cycle, but it should be zero because it has already been taken into account. This is done because the esd of this number is still of interest even when there is no longer a single racemic twinning parameter. It should be noted that because of the way the twin component factors are defined, there will inevitably be very large (e.g. 0.99) correlation coefficients between BASF parameters j and j+m in this treatment of combined normal and racemic twinning. For both the TWIN and HKLF 5 treatments, the data are reduced to the prime component by multiplying Fo^2 and Fc^2 by the ratio Fc^2(prime) / Fc^2(total) before performing the analysis of variance and Fourier calculations. Similarly 'OMIT h k l' refers to the indices of the prime component. The prime component is the one for which the indices have not been transformed by the TWIN instruction (i.e. m = 1 ), or in the case of HKLF 5 the component given with positive m (i.e. last, but not necessarily with |m| = 1). EXTI x [0] An extinction parameter x is refined by least-squares, where Fc is multiplied by: -1/4 k [ 1 + 0.001 * x * Fc^2 * lambda^3 / sin(2theta) ] where k is the overall scale factor. Note that it has been necessary to change this expression from SHELX-76 (which used an even cruder approximation) and SHELXTL (which used 0.002 instead of 0.001*lambda^3). The wavelength dependence is needed for HKLF 2 (Laue) data. The program will print a warning if extinction (or SWAT - see below) may be worth refining, but it is not normally advisable to introduce it until all the non-hydrogen atoms have been found. For twinned and powder data, the Fc^2 value used in the above expression is based on the total calculated intensity summed over all components rather than the individual contributions, which would be easier to justify theoretically (but makes little difference in practice). For the analysis of variance and '.fcf' output file, the Fo^2 values are brought onto the absolute scale of Fc^2 by dividing them by the scale factor(s) and the extinction factor. The above expression for the extinction is empirical and represents a compromise to cover both primary and secondary extinction; it has been shown to work well in practice but does not appear to correspond exactly to any of the expressions discussed in the literature. The article by A.C. Larson in Crystallographic Computing (1970), Ed. F.R. Ahmed, Munksgaard, Copenhagen, pp. 291-294 comes closest and should be consulted for further information. SWAT g [0] U [2] The SWAT option introduces one variable g and one fixed parameter U which enable diffuse solvent to be modeled by Babinet's principle (R. Langridge, D.A. Marvin, W.E. Seeds, H.R. Wilson, C.W. Hooper, M.H.F. Wilkins and L.D. Hamilton, J. Mol. Biol. 2 (1960) 38-64; H. Driessen, M.I.J. Haneef, G.W. Harris, B. Howlin, G. Khan and D.S. Moss, J. Appl. Cryst. 22 (1989) 510-516). The real part of the scattering factor for each non-hydrogen atom is modified as follows: f(new) = f(old) - g . exp [ -8pi^2.U.(sintheta/lambda)^2 ] The large value of U ensures that only the low theta f and hence Fc^2 values are affected. Subtracting the term in g in this way from the occupied regions of the structure is equivalent to adding a corresponding diffuse scattering term in the (empty) solvent regions in its effect on all calculated Fc^2 values except F(000) (which is calculated ignoring g). For proteins g usually refines to a value between 2 and 4; for small molecules without significant diffuse solvent regions it should refine to zero. Since both extinction and diffraction from diffuse solvent tend to affect primarily the strong reflections at low diffraction angle, they tend to show the same symptoms in the analysis of variance, and so a combined warning message is printed. It will however be obvious from the type of structural problem which of the two should be applied. The program does not permit the simultaneous refinement of SWAT and EXTI. MERG n [2] If n is equal to 2 the reflections are sorted and merged before refinement; if the structure is non-centrosymmetric the Friedel opposites are not combined before refinement (necessary distinction from SHELXS). If n is 1 the indices are converted to a 'standard setting' in which l is maximized first, followed by k, and then h; if n is zero, the data are neither sorted nor converted to a standard setting. n = 3 is the same as n = 2 except that Friedel opposites are also merged (this introduces small systematic errors and should only be used for good reason, e.g. to speed up the early stages of a refinement of a light atom structure before performing the final stages with MERG 2). Note that the reflections are always merged, and Friedel opposites combined, before performing Fourier calculations in SHELXL-93 so that the (difference) electron density is correctly scaled. Even with n = 0 the program will change the reflection order within each data block to optimize the vectorization of the structure factor calculations (it is shuffled back into the MERG order for LIST 4 output). Note that MERG may not be used in conjunction with TWIN or HKLF 5 or 6. In SHELX-76, MERG 3 had a totally different meaning, namely the determination of inter-batch scale factors; in SHELXL-93, these may be included in the refinement using the BASF instruction. ATOM LISTS AND LEAST-SQUARES CONSTRAINTS Atom instructions begin with an atom name (up to 4 characters which do not correspond to any of the ca. 80 SHELXL-93 or SHELXA command names, and terminated by at least one blank) followed by a scattering factor number (which refers to the list defined by the SFAC instruction(s)), x, y, and z in fractional coordinates, and (optionally) a site occupation factor (s.o.f.) and an isotropic U or six anisotropic Uij components (both in Angstroms^2). Note that different program systems may differ in their order of Uij components; SHELXL-93 uses the same order as SHELX-76 and SHELXTL. The exponential factor takes the form exp(-8.pi^2.U.[sin(theta)/lambda]^2) for an isotropic displacement parameter U and: exp ( -2.pi^2.[ h^2.(a*)^2.U11 + k^2.(b*)^2.U22 + ... + 2hk.a*.b*.U12 ] ) for anisotropic Uij. An atom is specified as follows in the '.ins' file: atomname sfac x y z sof [11] U [0.05] or U11 U22 U33 U23 U13 U12 The atom name must be unique, except that atoms in different residues - see RESI - may have the same names; in contrast to SHELX-76 it is not necessary to pad out the atom name to 4 characters with blanks. To fix any atom parameter, add 10. Thus the site occupation factor is normally given as 11 (i.e. fixed at 1). The site occupation factor for an atom in a special position should be multiplied by the multiplicity of that position (as given in International Tables, Volume A) and divided by the multiplicity of the general position for that space group. This is the same definition as in SHELX-76 and is retained for upwards compatibility; it might have been less confusing to keep the multiplicity and occupation factor separate. An atom on a fourfold axis for example will usually have s.o.f. = 10.25. If any atom parameter is given as (10*m+p), where abs(p) is less than 5 and m is an integer, it is interpreted as p*fv(m), where fv(m) is the mth 'free variable' (see FVAR). Note that there is no fv(1), since this position on an FVAR instruction is occupied by the overall scale factor, and m=1 corresponds to fixing an atom by adding 10. If m is negative, the parameter is interpreted as p*(fv(-m)-1). Thus to constrain two occupation factors to add up to 0.25 (for two elements occupying the same fourfold special position) they could be given as 20.25 and -20.25, i.e. 0.25*fv(2) and 0.25*(1-fv(2)), which correspond to p=0.25, m=2 and p=-0.25, m=-2 respectively. In SHELX-76, it was necessary to use free variables and coordinate fixing in this way to set up the appropriate constraints for refinement of atoms on special positions. In SHELXL-93, this is allowed (for upwards compatibility) but is NOT NECESSARY: the program will automatically work out and apply the appropriate positional, s.o.f. and Uij constraints for any special position in any space group, in a conventional setting or otherwise. Thus all that is necessary is to specify atomname, sfac, x, y and z, and leave the rest to the program; when the atom is (later) made anisotropic using the ANIS command, the appropriate Uij constraints will be added. For a well-behaved structure, the list of atom coordinates (from direct methods and/or difference electron density syntheses) suffices. If the multiplicity factor (s.o.f.) is left out, it will be fixed at the appropriate value of 1 for a general position and less than 1 for a special position. Since SHELXL-93 automatically generates origin restraints for polar space groups, no atom coordinates should be fixed by the user for this purpose (in contrast to SHELX-76). It may still be necessary to apply constraints by hand to handle disorder; a common case is that there are two possible positions for a group of atoms, in which the first set should all have s.o.f.'s of (say) 21, and the second set -21, with the result that the sum of the two occupation factors is fixed at 1, but the individual values may refine as fv(2) and 1-fv(2). Similarly if a special position with 2/m symmetry is occupied by Ca2+ and Ba2+, the two ions could be given the s.o.f.'s 30.25 and -30.25 respectively. In this case it would be desirable to use the EADP instruction to equate the Ca2+ and Ba2+ (anisotropic) displacement parameters. If U is given as -T, where T is in the range 0.5 < T < 5, it is fixed at T times U(eq) of the previous atom not constrained in this way. The resulting value is not refined independently but is updated after every least-squares cycle. SPEC del [0.2] All following atoms (until the next SPEC instruction) are considered to lie on special positions (for the purpose of automatic constraint generation) if they lie within del Angstroms of a special position. The coordinates of such an atom are also adjusted so that it lies exactly on the special position. RESI class [ ] number [0] alias Until the next RESI instruction, all atoms are considered to be in the specified 'residue', which may be defined by a class (up to four characters, beginning with a letter) or number (up to four digits) or both. The same atom names may be employed in different residues, enabling them to be referenced globally or selectively. The residue number should be unique to a particular residue, but the class may be used to refer to a class of similar residues, e.g. a particular type of amino acid in a polypeptide. Residues may be referenced by any instruction which allows atom names; the reference takes the form of the character '_' followed by either the residue class or number without intervening spaces. If an instruction codeword is followed immediately by a residue number, all atom names referred to in the instruction are assumed to belong to that residue unless they are themselves immediately followed by '_' and a residue number, which is then used instead. Thus: RTAB_4 Ang N H0 O_11 would cause the calculation of an angle N_4 - H0_4 - O_11, where the first two atoms are in residue 4 and the third is in residue 11. If the instruction codeword is followed immediately by a residue class, the instruction is effectively duplicated for all residues of that class. '_*' may be used to match all residue classes; this includes the default class ' ' (residue number 0) which applies until the first RESI instruction is encountered. Thus: MPLA_phe CB > CZ would calculate least-squares planes through atoms CB to CZ inclusive of all residues of class 'phe' (phenylalanine). In the special case of HFIX, only the FIRST instruction which applies to a given atom is applied. Thus: HFIX_1 33 N HFIX_* 43 N would add hydrogens to the N-terminal nitrogen (residue 1) of a polypeptide to generate a -NH3+ group, but all other (amide) nitrogens would become -NH-. Individual atom names in an instruction may be followed by '_' and a residue number, but not by '_*' or '_' and a residue class. If an atom name is not followed by a residue number, the current residue is assumed (unless overridden by a global residue number or class appended to the instruction codeword). The symbols '_+' meaning 'the next residue' and '_-' meaning 'the preceding residue' (i.e. residues number n+1 and n-1 if the current residue number is n) may be appended to atom names but not to instruction codenames. Thus the instruction: RTAB_* Omeg CA_- C_- N CA could be used to calculate all the peptide (omega) torsion angles in a protein or polypeptide. If (as at the N-terminus in this example) some or all of the named atoms cannot be found for a particular residue, the instruction is simply ignored for that residue. '_$n' does not refer to a residue; it uses the symmetry operation $n defined by a preceding 'EQIV $n' instruction to generate an equivalent of the named atom (see EQIV). alias specifies an alternative value of the residue number so that cyclic chains of residues may be created; for a cyclic pentapeptide (residue numbers 2,3,..6) it could be set to 1 for residue 6 and to 7 for residue 2. If more than one RESI instruction refers to the same number, alias only needs to be specified once. alias is referenced only by the _+ and _- operations (see above), and a value used for alias may not be used as a residue number on a RESI instruction. Note that if there is more than one cyclic peptide in the asymmetric unit, it is a good idea to leave a gap of TWO residue numbers between them. E.g. a cyclic pentapeptide with two molecules in the asymmetric unit would be numbered 2 to 6 and 9 to 13, with aliases 7 on RESI 2, 1 on RESI 6, 14 on RESI 9 and 10 on RESI 13. It will generally be found convenient for applying restraints etc. to use the same names for atoms in identical residues. MOVE dx [0] dy [0] dz [0] sign [1] The coordinates of the following atoms are changed to: x = dx + sign * x, y = dy + sign * y, z = dz + sign * z until superseded by a further MOVE. MOVE should not be used at the same time as the specification of zero coordinates to indicate that an atom should not be used in fitting a fragment of known geometry (e.g. AFIX 66), because after the move the coordinates will no longer be zero! ANIS n The next n isotropic non-hydrogen atoms are made anisotropic, generating appropriate special position constraints for the Uij if required. Intervening atoms which are already anisotropic are not counted. A negative n has the same effect. ANIS names The named atoms are made anisotropic (if not already), generating the appropriate constraints for special positions. Note that names may include '$' followed by a scattering factor name (see SFAC); 'ANIS $CL' would make all chlorine atoms anisotropic. Since ANIS, like other instructions, applies to the current residue unless otherwise specified, ANIS_* $S would be required to make the sulfur atoms in all residues anisotropic (for example). ANIS MUST precede the atoms to which it is to be applied. ANIS on its own, with neither a number nor names as parameters, makes all FOLLOWING non-hydrogen atoms (in all residues) anisotropic. The L.S. and CGLS instructions provide the option of delaying the conversion to anisotropic of all atoms specified by ANIS until a given number of least-squares cycles has been performed. AFIX mn d [#] sof [11] U [10.08] AFIX applies constraints and/or generates idealized coordinates for all atoms until the next AFIX instruction is read. The digits mn of the AFIX code control two logically quite separate operations. Although this is confusing for new users, it has been retained for upwards compatibility with SHELX-76, and because it provides a very concise notation. m refers to geometrical operations which are performed before the first refinement cycle (hydrogen atoms are idealized before every cycle), and n sets up constraints which are applied throughout the least-squares refinement. n is always a single digit; m may be two, one or zero digits (the last corresponds to m = 0). The options for idealizing hydrogen atom positions depend on the connectivity table which is set up using CONN, BIND, FREE and PART; with experience, this can also be used to generate hydrogen atoms attached to disordered groups and to atoms on special positions. d determines the bond lengths in the idealized groups, and sof and U OVERRIDE the values in the atom list for all atoms until the next AFIX instruction. U is not applied if the atom is already anisotropic, but is used if an isotropic atom is to be made anisotropic using ANIS. Any legal U value may be used, e.g. 31 (a free variable reference) or -1.2 (1.2 times Ueq of the preceding normal atom). Each AFIX instruction must be followed by the required number of hydrogen or other atoms. The individual AFIX options are as follows; the default X-H distances depend on both the chemical environment and the temperature (to allow for librational effects) which is specified by means of the TEMP instruction. m = 0 No action. m = 1 Idealized tertiary C-H with all X-C-H angles equal. There must be three and only three other bonds in the connectivity table to the immediately preceding atom, which is assumed to be carbon. m = 1 is often combined with a riding model refinement (n = 3). m = 2 Idealized secondary CH2 with all X-C-H and Y-C-H angles equal, and H-C-H determined by X-C-Y (i.e. approximately tetrahedral, but widened if X-C-Y is much less than tetrahedral). This option is also suitable for riding refinement (n = 3). m = 3 Idealized CH3 group with tetrahedral angles. The group is staggered with respect to the shortest other bond to the atom to which the -CH3 is attached. If there is no such bond (e.g. an acetonitrile solvent molecule) this method cannot be used (but m = 13 is still viable). m = 4 Aromatic C-H or amide N-H with the hydrogen atom on the external bisector of the X-C-Y or X-N-Y angle. m = 4 is suitable for a riding model refinement, i.e. AFIX 43 before the H atom. m = 5 Next five non-hydrogen atoms are fitted to a regular pentagon, default d = 1.42 A. m = 6 Next six non-hydrogen atoms are fitted to a regular hexagon, default d = 1.39 A. m = 7 Identical to m = 6 (included for upwards compatibility from SHELX-76). In SHELX-76 only the first, third and fifth atoms of the six-membered ring were used as target atoms; in SHELXL-93 this will still be the case if the other three are given zero coordinates, but the procedure is more general because any one, two or three atoms may be left out by giving them zero coordinates. m = 8 Idealized OH group, with X-O-H angle tetrahedral. If the oxygen is attached to a saturated carbon, all three staggered positions are considered for the hydrogen. If it is attached to an aromatic ring, both positions in the plane are considered. The final choice is based on forming the 'best' hydrogen bond to a nitrogen, oxygen, chlorine or fluorine atom. The algorithm involves generating a potential position for such an atom by extrapolating the O-H vector, then finding the nearest N, O, F or Cl atom to this position, taking symmetry equivalents into account. If another atom which, (according to the connectivity table) is bonded to the N, O, F or Cl atom, is nearer to the ideal position, the N, O, F or Cl atom is not considered. Note that m = 8 had a different effect in SHELX-76 (but was rarely employed). m = 9 Idealized terminal X=CH2 or X=NH2+ with the hydrogen atoms in the plane of the nearest substituent on the atom X. Suitable for riding model refinement (AFIX 93 before the two H atoms). m = 10 Idealized pentamethylcyclopentadienyl (Cp*). This AFIX must be followed by the 5 ring carbons and then the 5 methyl carbons in cyclic order, so that the first methyl group (atom 6) is attached to the first carbon (atom 1). The default d is 1.42 A, with the C-CH3 distance set to 1.063d. A variable-metric rigid group refinement (AFIX 109) would be appropriate, and would allow for librational shortening of the bonds. Hydrogen atoms (e.g. with AFIX 37 or 127) may be included after the corresponding carbon atoms, in which case AFIX 0 or 5 (in the case of a rigid group refinement) must be inserted before the next carbon atom. m = 11 Idealized naphthalene group with equal bonds (default d = 1.39 A). The atoms should be numbered as a symmetrical figure of eight, starting with the alpha C and followed by the beta, so that the first six atoms (and also the last six) describe a hexagon in cyclic order. m = 11 is also appropriate for rigid group refinement (AFIX 116). m = 12 Idealized disordered methyl group; as m = 3 but with two positions rotated from each other by 60 degrees. The corresponding occupation factors should normally be set to add up to one, e.g. by giving them as 21 (i.e. 1*fv(2) ) and -21 ( 1*(1-fv(2)) ). If HFIX is used to generate an AFIX instruction with m=12, the occupation factors are fixed at 0.5. AFIX 12n is suitable for a para methyl on a phenyl group with no meta substituents, and should be followed by 6 half hydrogen atoms (first the three belonging to one -CH3 component, then the three belonging to the other, so that hydrogens n and n+3 are opposite one another). Disordered -CF3 groups may also be generated in this way (with d=1.32). m = 13 Idealized CH3 group with tetrahedral angles. If the coordinates of the first hydrogen atom are non-zero, they define the torsion angle of the methyl group. Otherwise (or if the AFIX instruction is being generated via HFIX) a structure-factor calculation is performed (of course only once, even if many hydrogens are involved) and the torsion angle is set which maximizes the sum of the electron density at the three calculated hydrogen positions. Since even this is not an infallible method of getting the correct torsion angle, it should normally be combined with a rigid or rotating group refinement for the methyl group (e.g. mn = 137 before the first H). In subsequent least- squares cycles the group is re-idealized retaining the current torsion angle. -CF3 groups may be generated in the same way (with d = 1.32). m = 14 Idealized OH group, with X-O-H angle tetrahedral. If the coordinates of the hydrogen atom are non-zero, they are used to define the torsion angle. Otherwise (or if HFIX was used to set up the AFIX instruction) the torsion angle is chosen which maximizes the electron density (see m = 13). Since this torsion angle is unlikely to be very accurate, the use of a rotating group refinement is recommended (i.e. mn = 147 before the H atom). m = 15 BH group in which the boron atom is bonded to either four or five other atoms as part of an polyhedral fragment. The hydrogen atom is placed on the vector which represents the negative sum of the unit vectors along the four or five other bonds to the boron atom. m = 16 Acetylenic C-H, with X-C-H linear. Usually refined with the riding model, i.e. AFIX 163. m > 16 A group defined in a FRAG...FEND section with code = m is fitted, usually as a preliminary to rigid group refinement. The FRAG...FEND section MUST precede the corresponding AFIX instruction in the '.ins' file, but there may be any number of AFIX instructions with the same m corresponding to a single FRAG...FEND section. When a group is fitted (m = 5, 6, 10 or 11, or m > 16), atoms with non-zero coordinates are used as target atoms with equal weight. Atoms with all three coordinates zero are ignored. Any three or more non-colinear atoms may be used as target atoms. 'Riding' (n = 3, 4) and 'rotating' (n = 7, 8) hydrogen atoms, but not other idealized groups, are re-idealized (if m is 1, 2, 3, 4, 8, 9, 12, 13, 14, 15 or 16) before each refinement cycle (after the first cycle, the coordinates of the first hydrogen of a group are always non-zero, so the torsion angle is retained on reidealizing). For n = 4 and 8, the angles are reidealized but the (refined) X-H bond length is retained, unless the hydrogen coordinates are all zero, in which case d (on the AFIX instruction) or (if d is not given) a standard value which depends on the chemical environment and temperature (TEMP) is used instead. n = 0 No action. n = 1 The coordinates, s.o.f. and U or Uij are fixed. n = 2 The s.o.f. and U (or Uij) are fixed, but the coordinates are free to refine. n = 3 The coordinates, but not the s.o.f. or U (or Uij) 'ride' on the coordinates of the previous atom with n not equal to 3. The same shifts are applied to the coordinates of both atoms, and both contribute to the derivative calculation. The atom on which riding is performed may not itself be a riding atom, but it may be in a rigid group (m = 5, 6 or 9). n = 4 This constraint is the same as n = 3 except that the X-H distance is free to refine. The X-H vector direction does not change. This constraint requires better quality reflection data than n = 3, but allows for variations in apparent X-H distances caused by libration and bonding effects. If there is more than one equivalent hydrogen, the same shift is applied to each equivalent X-H distance (e.g. to all three C-H bonds in a methyl group). n = 4 may be combined with DFIX or SADI restraints (to restrain chemically equivalent X-H distances to be equal) or embedded inside a rigid (n = 6) group, in which case the next atom (if any) in the same rigid group must follow an explicit AFIX instruction with n = 5. Note that n = 4 had a different effect in SHELX-76. n = 5 The next atom(s) are 'dependent' atoms in a rigid group. Note that this is automatically generated for the atoms following an n = 6 or n = 9 atom, so does not need to be included specifically unless m has to be changed (e.g. AFIX 35 before the first hydrogen of a rigid methyl group with AFIX 6 or 9 before the preceding carbon). n = 6 The next atom is the 'pivot atom' of a NEW rigid group, i.e. the other atoms in the rigid group rotate about this atom, and the same translational shifts are applied to all atoms in the rigid group. n = 7 The following (usually hydrogen) atoms (until the next AFIX with n not equal to 7) are allowed to ride on the immediately preceding atom X and rotate about the Y-X bond; X must be bonded to one and only one atom Y in the connectivity list, ignoring the n = 7 atoms (which, if they are F rather than H, may be present in the connectivity list). The motion of the atoms of this 'rotating group' is a combination of riding motion (c.f. n = 3) on the atom X plus a tangential component perpendicular to the Y-X and X-H bonds, so that the X-H distances, Y-X-H and H-X-H angles remain unchanged. This constraint is intended for -OH, -CH3 and possibly -CF3 groups. X may be part of a rigid group, which may be resumed with an AFIX n = 5 following the n = 7 atoms. n = 8 This constraint is similar to n = 7 except that the X-H distances may also vary, the same shifts being applied along all the X-H bonds. Thus only the Y-X-H and H-X-H angles are held constant; the relationship of n = 8 to n = 7 corresponds to that of n = 4 to n = 3. DFIX and SADI restraints may be useful for the X-H distances. This constraint is useful for -CF3 groups or for -CH3 groups with good data. n = 9 The first (pivot) atom of a new 'variable metric' rigid group. Such a group retains its 'shape' but may shrink or expand uniformly. It is useful for C5H5 and BF4 groups, which may show appreciable librational shortening of the bond lengths. Subsequent atoms of this type of rigid group should have n = 5, which is generated automatically by the program if no other AFIX instruction is inserted between the atoms. Riding atoms are not permitted inside this type of rigid group. Only the pivot atom coordinates may be fixed (by adding 10) or tied to free variables, and only the pivot atom may lie on a special position (for the automatic generation of special position constraints). Although there are many possible combinations of m and n, in practice only a small number is used extensively, as discussed in the section on hydrogen atoms. Rigid group fitting and refinement (e.g. AFIX 66 followed by six atoms of a phenyl ring or AFIX 109 in front of a Cp* group) is particularly useful in the initial stages of refinement; atoms not found in the structure solution may be given zero coordinates, in which cases they will be generated from the rigid group fit. A rigid group or set of dependent hydrogens must ALWAYS be followed by 'AFIX 0' (or another AFIX instruction)! Leaving out 'AFIX 0' by mistake is a common cause of error; the program is able to detect and correct some obvious cases, but in many cases this is not logically possible. HFIX mn U [#] d [#] atomnames HFIX generates AFIX instructions and dummy hydrogen atoms bonded to the named atoms, the AFIX parameters being as specified on the HFIX instruction. This is exactly equivalent to the corresponding editing of the atom list. The atom names may reference residues (by appending '_n' to the name, where n is the residue number), or SFAC names (preceded by a '$' sign). U may be any legal value for the isotropic temperature factor, e.g. 21 to tie a group of hydrogen U value to free variable 2, or -1.5 to fix U at 1.5 times U(eq) of the preceding normal atom. HFIX MUST precede the atoms to which it is to be applied. If more than one HFIX instruction references a given atom, only the FIRST is applied. 'HFIX 0' is legal, and may be used to switch off following HFIX instructions for a given atom (which is useful if the latter involve '_*' or a global reference to a residue class). FRAG code [17] a [1] b [1] c [1] alpha [90] beta [90] gamma [90] Enables a fragment to be input using a cell and coordinates taken from the literature. Orthogonal coordinates may also be input in this way. Such a fragment may be fitted to the set of atoms following an AFIX instruction with m = code (code must be greater than 16); there must be the same number of atoms in this set as there are following FRAG, and they must be in the same order. Only the coordinates of the FRAG fragment are actually used; atom names, sfac numbers, sof and Uij are IGNORED. A FRAG fragment may be given anywhere between UNIT and HKLF or END, and must be terminated by a FEND instruction, but must precede any AFIX instruction which refers to it. This 'rigid fit' is often a preliminary to a rigid group refinement (AFIX with n = 6 or 9). FEND This must immediately follow the last atom of a FRAG fragment. EXYZ atomnames The same x, y and z parameters are used for all the named atoms. This is useful when atoms of different elements share the same site, e.g. in minerals (in which case EADP will probably be used as well). The coordinates (and possibly free variable references) are taken from the named atom which precedes the others in the atom list, and the actual values, free variable references etc. given for the x, y and z of the other atoms are ignored. An atom should not appear in more than one EXYZ instruction. EADP atomnames The same isotropic or anisotropic displacement parameters are used for all the named atoms. The displacement parameters (and possibly free variable references) are taken from the named atom which precedes the others in the atom list, and the actual values, free variable references etc. given for the Uij of the other atoms are ignored. The atoms involved must either be all isotropic or all anisotropic. An atom should not appear in more than one EADP instruction. 'Opposite' fluorines of PF6 or disordered -CF3 groups are good candidates for EADP, e.g. EADP F11 F14 EADP F12 F15 EADP F13 F16 C1 ....... PART 1 F11 ...... 21 ...... F12 ...... 21 ...... F13 ...... 21 ...... PART 2 F14 ...... -21 ...... F15 ...... -21 ...... F16 ...... -21 ...... PART 0 EADP applies an (exact) CONSTRAINT. The SIMU instruction RESTRAINS the Uij components of neighboring atoms to be approximately equal with an appropriate (usually fairly large) esd. EQIV $n symmetry operation Defines symmetry operation $n for referencing symmetry equivalent atoms on any instruction which allows atom names, by appending '_$n' (where n is an integer between 1 and 511 inclusive) to the atom name. Such a symmetry operation must be defined before it is used; it does not have to be an allowed operation of the space group, but the same notation is used as on the SYMM instruction. The same $n may not appear on two separate EQIV instructions. Thus: EQIV $2 1-x, y, 1-z CONF C1 C2 C2_$2 C1_$2 could be used to calculate a torsion angle across a crystallographic twofold axis (note that this may be required because CONF with no atom names only generates torsion angles automatically which involve the unique atom list and a one atom deep shell of symmetry equivalents). If the instruction codeword refers to a residue, this is applied to the named atoms before any symmetry operation specified with '_$n'. Thus: RTAB_23 O..O OG_12 O_$3 would calculate the (hydrogen bond) distance between OG_12 and (O_23)_$3, i.e. between OG in residue 12 and the equivalent obtained by applying the symmetry operation defined by EQIV $3 to the atom O in residue 23. OMIT atomnames The named atoms are retained in the atom list but ignored in the structure factor calculation and least-squares refinement. This instruction may be used, together with L.S. 0 and FMAP 2, to create an 'OMIT map' to get a clearer picture of disordered regions of the structure; this concept will be familiar to macromolecular crystallographers. In particular, 'OMIT $H' can be used to check the hydrogen atom assignment of -OH groups etc. If an actual peak is present within 0.31 A of the calculated hydrogen atom position, the electron density appears in the 'Peak' column of the PLAN output. OMIT_* $H must be used for this if residues are employed. THE CONNECTIVITY LIST The connectivity list is a list of 'bonds' which is set up automatically, and may be edited using BIND and FREE. It is used to define idealized hydrogen atom positions, for the BOND and PLAN output of bond lengths and angles, and by the instructions DELU, CHIV, SAME and SIMU. Hydrogen atoms are excluded from the connectivity list (except when introduced by hand using BIND). CONN bmax [12] r [#] atomnames or CONN bmax [12] The CONN instruction fine tunes the generation of the connectivity table and is particularly useful when pi-bonded ligands or metal ions are present in the structure. For the purposes of the connectivity table (which is always generated), bonds are all distances between non-hydrogen atoms less than r1 + r2 + 0.5 Angstroms, where r1 and r2 are the covalent radii of the atoms in question (taking PART into consideration as explained below). A shell of symmetry equivalent atoms is also generated, so that all unique bonds are represented at least once in the list. All bonds, including those to symmetry equivalent atoms, may be deleted or added using the FREE or BIND instructions. Default values of r (identified by the scattering factor type) are stored in the program. These defaults may be changed (for both the connectivity table AND the PLAN -n output) by using the full form of the SFAC instruction. Alternatively the defaults may be overridden for the named atoms by specifying r on a CONN instruction, in which case r is used in the generation of the connectivity list but not by the PLAN instruction. '$' followed by an element name (the same as on a SFAC instruction) may also be employed on a CONN instruction (and also does not apply to PLAN). The second form of the CONN instruction may be used to change the maximum coordination number bmax for all atoms (which defaults to 12 if there is no CONN instruction). If, after generating bonds as above and editing with FREE and BIND, there are more than bmax bonds to a given atom, the list is pruned so that only the shortest bmax are retained. A harmless side-effect of this pruning of the connectivity list is that symmetry operations may be stored and printed that are never actually used. Note that this option only removes one entry for a bond from the connectivity list, not both, except in the case of 'CONN 0' which ensures that there are no bonds to or from the named atoms. In some cases it will be necessary to use FREE to remove a 'bond' from a light atom to an alkali metal atom (for example) in order to generate hydrogen atoms correctly. 'CONN 0' is frequently used to prevent the solvent water in macromolecular structures from making additional 'bonds' to the macromolecule which confuse the generation of idealized hydrogen atoms etc., and it is also required if BUMP is used to generate 'antibumping' restraints in such cases. Refinements of macromolecules will often include BUMP and 'CONN 0 O1 > LAST', where 'LAST' may be used to indicate the last atom in the file (which saves trouble when adding extra waters). The CONN instruction, like ANIS and HFIX, MUST precede the atoms to which it is to be applied. Repeated CONN instructions are allowed; the LAST relevant CONN preceding a particular atom is the one which is actually applied. CONN without atom names changes the default value of bmax for all following atoms. The following example illustrates the use of CONN: CONN Fe 0 MPLA 5 C11 > C15 Fe MPLA 5 C21 > C25 Fe Fe ..... C11 ..... ......... C25 ..... which would prevent bonds being generated from the iron atom to all 10 carbons in ferrocene. In this example the distances of the iron atom from the two ring planes would be calculated instead. PART n sof The following atoms belong to part n of a disordered group. The automatic bond generation ignores bonds between atoms with different PART numbers, unless one of them is zero (the value before the first PART instruction). If a site occupation factor (sof) is specified on the PART instruction, it overrides the value on the following atom instructions (even if set via an AFIX instruction) until a further PART instruction, e.g. 'PART 0', is encountered). If n is negative, the generation of special position constraints is suppressed and bonds to symmetry generated atoms with the same or a different non-zero PART number are excluded; this is suitable for a solvent molecule disordered on a special position of higher symmetry than the molecule can take (e.g. a toluene molecule on an inversion center). A PART instruction remains in force until a further PART instruction is read; 'PART 0' should be used to continue with the non-disordered part of the structure. Some care is necessary in generating hydrogen atoms where disordered groups are involved. If the hydrogen atoms are assigned a PART number, then even if the atom to which they are attached has no part number (i.e. PART 0) the above rules may be used by the program to work out the correct connectivity for calculating the hydrogen atom positions. HFIX hydrogens are assigned the PART number of the atom to which they are attached. If the hydrogens and the atom to which they are attached belong to PART zero but the latter atom is bonded to atoms with non-zero PART, the LOWEST of these non-zero PART numbers is assumed to be the major component and is used to calculate the hydrogen positions. As an example, assume that one of the valine residues (Val32) in a small protein is disordered so that one of the methyl groups is common to both components and the other is disordered unequally over the two remaining positions. Hydrogens could be added for the major component only as follows: HFIX_val 37 CG1 CG2 HFIX_val 13 CB : RESI 32 Val N ..... CA ..... C ..... O ..... CB ..... CG1 ..... PART 1 CG2 1 ... ... ... 21 ... PART 2 CG2' 1 ... ... ... -21 ... PART 0 : where free variable 2 is the occupation factor for PART 1 (say 0.7) and the occupation factor of the second component is tied to 1-fv(2) (i.e. 0.3). The value for this free variable is set on the FVAR instruction and is free to refine. If there were more than two components, a linear free variable restraint (SUMP) could be used to restrain the sum of occupation factors to (e.g.) 1. The hydrogens for the second component could be added in a subsequent job with the help of AFIX instructions: : CB ..... PART 1 ! This hydrogen for the major component was AFIX 13 ! generated in the previous run (but Part 1 HB 2 ... ... ... 21 -1.2 ! must be added and its sof changed now !). PART 2 !! AFIX 13 !! These four lines are added now; HFIX HB' 2 ... ... ... -21 -1.2 !! would not be a valid alternative. PART 0 !! AFIX 0 CG1 ..... AFIX 37 ! HG1A 2 ... ... ... 11 -1.5 ! Generated from HFIX in previous run. HG1B 2 ... ... ... 11 -1.5 ! HG1C 2 ... ... ... 11 -1.5 ! AFIX 0 ! PART 1 CG2 1 ... ... ... 21 ... AFIX 37 ! HG2A 2 ... ... ... 21 -1.5 ! Generated from HFIX in previous run. HG2B 2 ... ... ... 21 -1.5 ! HG2C 2 ... ... ... 21 -1.5 ! AFIX 0 ! PART 2 CG2' 1 ... ... ... -21 ... AFIX 37 !! HG2D 2 ... ... ... -21 -1.5 !! These five lines are added now - in this HG2E 2 ... ... ... -21 -1.5 !! case HFIX 37 CG2'_32 could also be used. HG2F 2 ... ... ... -21 -1.5 !! AFIX 0 !! PART 0 : BIND atom1 atom2 The specified 'bond' (which may be of any length) is added to the connectivity list if it is not there already. Only one of the two atoms may be an equivalent atom (i.e. have the extension _$n). FREE atom1 atom2 The specified 'bond' is deleted from the connectivity list (if present). Only one of the two atoms may be an equivalent atom (i.e. have the extension _$n). LEAST-SQUARES RESTRAINTS DFIX d s [#] atom pairs The distance between the first and second named atom, the third and fourth, fifth and sixth etc. (if present) is restrained to a target value d with an estimated standard deviation s. d may refer to a 'free variable', otherwise it is considered to be fixed. Fixing d by adding 10 is not allowed, so the value may lie between 0 and 15. If d is given a negative sign, the restraint is applied ONLY if the current distance between the two atoms is LESS than |d|. This is an 'antibumping' restraint, and may be used to prevent solvent (water) molecules from approaching too close to one another or to a macromolecule. Antibumping restraints may also be generated automatically using the BUMP instruction (see below). The default value of s is 0.03 when d is positive and 0.1 when d is negative. The default s for positive d may be changed by means of a preceding DEFS instruction (see below). BUMP s [0.1] d1 [#] d2 [#] d3 [#] ... 'Antibumping' restraints are generated automatically for all (solvent water) atoms which have been flagged with 'CONN 0'. The restraints can be generated between CONN 0 atoms and all other non-hydrogen atoms, and appear in subsequent tables as DFIX instructions with negative d and effective standard deviation s. The values to be used for d are given in SFAC order as d1, d2, d3, ...; the default values are 3.2 for C, 2.7 for N, 2.6 for O and 3.5 for ALL other elements. If the structure contains atoms of other elements (e.g. explicit cations in polynucleotides) that can interact with the solvent, it will be necessary to specify the appropriate distances on the BUMP instruction. The restraints are also set up for all symmetry equivalents automatically; however if the sum of occupancies of the two atoms is less than 1.1, no restraint is generated. Iterative refinement with antibumping restraints, followed by deletion of atoms which persist in giving unacceptable distances or for which the (equivalent isotropic) displacement parameters become larger than say 1.0 to 1.2 A^2, and insertion of new potential solvent atoms from difference electron density syntheses, provides a reliable procedure for building up a solvent model with acceptable hydrogen bonding distances which is consistent with the diffraction data; 'PLAN 200 2.3' would be appropriate. If there are more than 15 different SFAC types, d15 is used for those with numbers greater than 15. SAME s1 [0.03] s2 [0.03] atomnames The list of atoms (which may include the symbol '>' meaning all intervening non-hydrogen atoms in a forward direction, or '<' meaning all intervening non-hydrogen atoms in a backward direction) is compared with the same number of atoms which follow the SAME instruction. All bonds in the connectivity list for which both atoms are present in the SAME list are restrained to be the same length as those between the corresponding following atoms (with an effective standard deviation s1). The same applies to 1-3 distances (defined by two bonds in the connectivity list which share a common atom), with standard deviation s2. If s2 is absent it is given the same value as s1. s1 or s2 may be set to zero to switch off the corresponding restraints. The program automatically sets up the n*(n-1)/2 restraint equations required when n interatomic distances should be equal. This ensures optimum efficiency and avoids arbitrary unequal weights. Only the minimum set of restraints needs to be specified in the '.ins' file; redundant restraints are ignored by the program, provided that they have the same sigma values as the unique set of restraints. See also SADI. The position of a SAME instruction in the input file is critical. If (say) all the phenylalanine residues in a protein are to be restrained to have the same 1,2 and 1,3 distances, and all have the same atom names (in the same order!), and the same residue name (PHE), but different residue numbers, then ONE SAME instruction suffices: SAME_phe N > CZ where the first atom in each phenylalanine is labeled 'N' and the last 'CZ'. This instruction should be inserted before the first atom (N) of the phenyl- alanine with the best geometry, because the connectivity table for this residue will be used to define the 1,2 and 1,3 distances. This phenylalanine does not have to be the first in the atom list. In this case it would also be reasonable to impose local twofold symmetry for the phenyl ring, so a further SAME instruction could be added before the beta (benzylic) carbon (CB) of the same residue: SAME CB CG CD2 CD1 CE2 CE1 CZ where the order of the immediately following atoms is: CB CG CD1 CD2 CE1 CE2 CZ. Note that these two SAME restraints are all that is required, however many PHE residues are present; the program will generate all indirectly implied 1,2 and 1,3 equal distance restraints! In this case it would also be sensible to make the carbon atoms of the benzyl groups coplanar by a FLAT restraint. SADI s [0.03] atom pairs The distances between the first and second named atoms, the third and fourth, fifth and sixth etc. (if present) are restrained to be equal with an effective standard deviation s. The SAME and SADI restraints are analyzed together by the program to find redundant and implied restraints. The same effect as is obtained using SADI can also be produced by using DFIX with d tied to a free variable, but the latter costs one more least-squares parameter (but in turn produces a value and esd for this parameter). The default effective standard deviations for SAME and SADI may be changed by means of a DEFS instruction before the instruction in question. CHIV V [0] s [0.2] atomnames The chiral volumes of the named atoms are restrained to the value V (in cubic Angstroms) with standard deviation s. The chiral volume is defined as the volume of the tetrahedron formed by the three bonds to each named atom, which must be bonded to three and only three non-hydrogen atoms in the connectivity list; the order in the connectivity list, which is determined by the order of increasing bond lengths, defines the sign of the chiral volume. Note that RTAB may be used to list chiral volumes defined in the same way but without restraining them. The chiral volume is positive for the alpha-carbon (CA) of an L-amino-acid if the order of the three bond lengths is CA-N, CA-C, CA-CB (as would be expected for an accurate structure). Note that 'CHIV 0' (or just CHIV since the default V is zero) may be used to impose a planarity restraint on an atom which is bonded to three others (by making the chiral volume zero), and is mathematically equivalent to a FLAT instruction which names the four atoms explicitly. FLAT s [0.2] four or more atoms If precisely four atoms are named, they are restrained to be coplanar (within the effective standard deviation s) by restraining the volume of the tetrahedron with the four atoms as corners to zero. The edges of this tetrahedron do NOT have to appear as bonds in the connectivity list. The algebra involved is the same as for CHIV (!), and so the units of s are Angstroms^3. If more than four atoms are specified, the fourth and all remaining atoms are used in turn as the fourth corner of a tetrahedron involving the first three atoms, for which the volume is again restrained to be zero. The first three atoms should be chosen so that they define a triangle for which the area is as large as possible; for example alternate atoms could be used for a six-membered ring. Although it might be objected that this method could cause the first three atoms to be 'more coplanar' than the others, in practice FLAT is a very simple and effective way of restraining a group of atoms to be approximately coplanar. Alternative methods involve either (a) biasing the plane towards the existing least-squares plane, (b) extra least-squares variables (which cost computer time), or (c) complicated calculations and problems with numerical precision. An alternative objection to this (and to some other) algorithms is that it will tend to cause the atoms to be 'attracted' towards one another (since this also reduces the volume of the tetrahedron). However this error becomes negligible as the atoms become nearly coplanar; tests with typical phenyl- alanine residues in a polypeptide showed that the bias introduced was of the order of 0.0001 Angstroms. The default value of s for CHIV and FLAT may be changed by a preceding DEFS instruction. DELU s1 [0.01] s2 [0.01] atomnames All bonds in the connectivity list connecting atoms on the same DELU instruction are subject to a 'rigid bond' restraint, i.e. the components of the (anisotropic) displacement parameters in the direction of the bond are restrained to be equal within an effective standard deviation s1. The same type of restraint is applied to 1-3 distances as defined by the connectivity list (atoms 1, 2 and 3 must all be defined on the same DELU instruction). If s2 is omitted it is given the same value as s1. A zero value for s1 or s2 switches off the corresponding restraint. If no atoms are specified, all non- hydrogen atoms are assumed. DELU is ignored if (in the refinement cycle in question) one or both of the atoms concerned is isotropic; in this case a 'hard' restraint is inappropriate, but SIMU may be used in the usual way as a 'soft' restraint. DELU without atomnames applies to all non-hydrogen atoms (in the current residue); DELU_* without atoms applies to all non-hydrogen atoms in all residues. SFAC element names may also be referenced, preceded by the symbol '$'. The default values of s1 and s2 may be changed by means of a preceding DEFS instruction. SIMU s [0.05] st [0.1] dmax [1.7] atomnames Atoms closer than dmax are RESTRAINED with effective standard deviation s to have the same Uij components. If (according to the connectivity table, i.e. ignoring attached hydrogens) one or both of the two atoms involved is terminal (or not bonded at all), st is used instead as the esd. If s but not st is specified, st is set to twice s. If no atoms are given, all non-hydrogen atoms are understood. SIMU_* with no atoms applies to all non-hydrogen atoms in all residues. SFAC element names may also be referenced, preceded by '$'. The interatomic distance for testing against dmax is calculated from the atom coordinates without using the connectivity table (though the latter is used for deciding if an atom is terminal or makes no bonds). Note that SIMU should in general be given a much larger esd (and hence lower weight) than DELU; whereas there is good evidence that DELU restraints should hold accurately for most covalently bonded systems, SIMU (and ISOR) are only rough approximations to reality. s or st may be set to zero to switch off the appropriate restraints. SIMU is intended for use for larger structures with poorer resolution and data to parameter ratios than are required for full unrestrained anisotropic refinement. It is based on the observation that the Uij values on neighboring atoms in larger molecules tend to be both similar and (when the resolution is poor) significantly correlated with one another. By applying a very weak restraint of this type, we allow a gradual increase and change in direction of the anisotropic displacement parameters as we go out along a side-chain, and we restrain the motion of atoms perpendicular to a planar group (which DELU cannot influence). The use of a distance criterion directly rather than via the connectivity table enables the restraints to be applied automatically to partially overlapping disordered atoms, for which it is an excellent approach. dmax can be set so that coordination distances to metal ions etc. are excluded. Terminal atoms tend to show the largest deviations from equal Uij's and so st should be set higher than s (or made equal to zero to switch off the restraints altogether). SIMU restraints are NOT recommended for SMALL molecules and ions, especially if free rotation or torsion is possible (e.g. C5H5-groups, AsF6- ions). For larger molecular fragments, the effective rotation angles are smaller, and the assumption of equal Uij for neighboring atoms is more appropriate: both translation and libration of a large fragment will result in relatively similar Uij components on adjacent atoms. SIMU may be combined with ISOR, which applies a further soft but quite different restraint on the Uij components. SIMU may also be used when one or both of the atoms concerned is isotropic. The default value of s may be changed by a preceding DEFS instruction (st is then set to twice s). DEFS sd [0.03] sf [0.2] su [0.01] ss [0.05] maxsof [1] DEFS may be used to change the default effective standard deviations for the following DFIX, SAME, SADI, CHIV, FLAT, DELU and SIMU restraints, and is useful when these are to be varied systematically to establish the optimum values for a large structure (e.g. using R(free)). sd is the default for s in the SADI and DFIX instructions (excluding DFIX instructions with negative d, for which the default s remains at 0.1), and also for s1 and s2 in the SAME instruction. sf is the default effective standard deviation for CHIV and FLAT, su is the default for both s1 and s2 in DELU, and ss is the default s for SIMU. The default st for SIMU is set to twice the default s. maxsof is the maximum allowed value that an occupation factor can refine to; occupation factors that are fixed or tied to free variables are not restricted. It is possible to change this parameter (to say 1.1 to allow for hydrogen atoms) when refining both occupation factors and U's for solvent water in proteins (a popular but not uncontroversial way of improving the R factor). ISOR s [0.1] st [0.2] atomnames The named atoms are RESTRAINED with effective standard deviation s so that their Uij components approximate to isotropic behavior; however the corresponding isotropic U is free to vary. ISOR is often applied, perhaps together with SIMU, to allow anisotropic refinement of large organic molecules when the data are not adequate for unrestrained refinement of all the Uij; in particular ISOR can be applied to solvent water for which DELU and SIMU are inappropriate. ISOR should in general be applied as a weak restraint, i.e. with relatively large sigmas, for the reasons discussed above (see SIMU); however it is also useful for preventing individual atoms from becoming 'non- positive-definite'. However it should not be used indiscriminately for this purpose without investigating whether there are reasons (e.g. disorder, wrong scattering factor type etc.) for the atom going n.p.d. If (according to the connectivity table, i.e. ignoring attached hydrogens) the atom is terminal (or makes no bonds), st is used instead as the esd. If s but not st is specified, st is set to twice s. If no atoms are given, all non-hydrogen atoms are understood. SFAC element names may also be referenced, preceded by '$'. s or st may be set to zero to switch off the appropriate restraints. ISOR without atom names (or ISOR_* if residues are used) applies this restraint to all non- hydrogen atoms. Note also the use of the keyword 'LAST' to indicate the last atom in the .ins file; an anisotropic refinement of a macromolecule will often include 'ISOR 0.1 O1 > LAST', which assumes that the solvent water is in residue 0 at the end of the atom list. Note that ISOR should in general be given a much larger esd (and hence lower weight) than DELU; whereas there is good evidence that DELU restraints should hold accurately for most covalently bonded systems, ISOR (and SIMU) are only rough approximations to reality. SUMP c sigma c1 m1 c2 m2 ... The linear restraint: c = c1*fv(m1) + c2*fv(m2) + ... is applied to the specified free variables. This enables more than two atoms to be assigned to a particular site, with the sum of site occupation factors restrained to be a constant. It also enables linear relations to be imposed between distances used on DFIX restraints, for example to restrain a group of atoms to be collinear. sigma is the effective standard deviation. By way of example, assume that a special position on a four-fold axis is occupied by a mixture of sodium, calcium, aluminium and potassium cations so that the average charge is +2 and the site is fully occupied. The necessary restraints and constraints could be set up as follows (the program will take care of the special position constraints on the coordinates and Uij of course): SUMP 1.0 0.01 1.0 2 1.0 3 1.0 4 1.0 5 ! site fully occupied SUMP 2.0 0.01 1.0 2 2.0 3 3.0 4 1.0 5 ! mean charge = +2 EXYZ Na1 Ca1 Al1 K1 ! common x, y and z coordinates EADP Na1 Ca1 Al1 K1 ! common U or Uij FVAR ... 0.20 0.30 0.35 0.15 ! starting values for free variables 2..5 ... Na1 ... ... ... ... 20.25 ... ! 0.25 * fv(2) [the 0.25 is required for Ca1 ... ... ... ... 30.25 ... ! 0.25 * fv(3) a special position on a Al1 ... ... ... ... 40.25 ... ! 0.25 * fv(4) four-fold axis, i.e. site K1 ... ... ... ... 50.25 ... ! 0.25 * fv(5) symmetry 4] Similar SUMP restraints may be used when elements are distributed over several sites in minerals so that the elemental composition corresponds (within suitable standard deviations) to an experimental chemical analysis. LEAST-SQUARES ORGANIZATION L.S. nls [0] nrf [0] nextra [0] maxvec [511] nls cycles of full-matrix least-squares refinement are performed, followed by a structure factor calculation. When L.S. (or CGLS) is combined with BLOC, each cycle involves refinement of a block of parameters which may be set up differently in different cycles. If no L.S. or CGLS instruction is given, 'L.S. 0' is assumed. If nrf is positive it is the number of these cycles which should be performed before applying ANIS. This two-stage refinement is particularly suitable for the early stages of least-squares refinement; experience indicates that it is not advisable to let everything go at once! Negative nrf indicates which reflections should be ignored during the refinement but used instead for the calculation of independent R-factors in the final structure factor summation; for example L.S. 4 -10 would ignore every 10th reflection for refinement purposes. The selection is based on the (merged) reflection list before applying OMIT and SHEL, and so should be independent of the operation of these two instructions (however only data which have not been suppressed by OMIT or SHEL contribute to the independent R-factors). This strategy should also make the selection of reflections to ignore independent of the computer. It is desirable to use the same negative value of nrf throughout, so that the values of 'R1(free)' and 'wR2(free)' are not biased by the 'memory' of the contribution of these reflections to earlier refinements. These independent R-factors may be used to calibrate the sigmas for the various classes of restraint, and provide a check as to whether the data are being 'over-refined' (primarily a problem for macromolecules with a poor data to parameter ratio). For further details see A.T. Brunger, Nature 355 (1992) 472-475. In SHELXL-93, these ignored reflections are treated in the same way as reflections suppressed with OMIT except for the calculation of R1(free) and wR2(free), i.e they are used in the calculation of R-indices based on all reflections, but not used for Fourier calculations. nextra is the number of additional parameters which were derived from the data when performing empirical absorption corrections etc. It should be set to 8 (LAMI), 12 (HOPE) or 18 (EMPI) if SHELXA was used for this purpose, and to 44 for DIFABS (or 34 without the theta correction; N. Walker and D. Stuart, Acta Cryst., A39 (1983) 158-166). It ensures that the standard deviations and GooF are estimated correctly; they would be underestimated if the number of extra parameters is not specified. nextra is zero (and so can be omitted) if extra information in the form of indexed crystal faces or psi-scan data was used to apply an absorption correction. maxvec refers to the maximum number of reflections processed simultaneously in the rate-determining calculations. Usually the program utilizes all available memory to process as many reflections as possible simultaneously, subject to a maximum of maxvec, which may not be larger than 511. For complicated reasons involving the handling of suppressed and 'R(free)' reflections and input/output buffering, some blocks may be smaller than the maximum, especially if the facilities for refinement against twinned or powder data are being used. It may be desirable to set maxvec to a smaller number than 511 to prevent unnecessary disk transfers when large structures are refined on virtual memory systems with limited physical memory. CGLS nls [0] nrf [0] nextra [0] maxvec [511] As L.S., but the Konnert-Hendrickson conjugate-gradient algorithm is employed instead of the full-matrix approach. Although BLOC may be used with CGLS, in practice it is much better to refine all parameters at once. CGLS is much faster than L.S. for a large number of parameters, and so will be the method of choice for most macromolecular refinements. The convergence properties of CGLS are good in the early stages (especially if there are many restraints), but cannot compete with L.S. in the final stages for structures which are small enough for full-matrix refinement. The major disadvantage of CGLS is that it does not provide estimated standard deviations, so when a large structure has been refined to convergence using CGLS it may be worth performing a blocked full-matrix refinement (L.S./BLOC) to obtain the standard deviations in quantities of interest (e.g. torsion angles, in which case only xyz blocks would be required). A further disadvantage of CGLS is its propensity for getting stuck in a local minimum in situations where L.S./BLOC would find the global minimum; for this reason a mixed CGLS/L.S. alternative is provided (CGLS with negative nls) which performs CGLS refinement in the odd numbered cycles and L.S. in the even numbered. When this option is used, it will be normal to provide BLOC instructions for the even numbered cycles only. The other parameters have the same meaning as with L.S.; CGLS is entirely suitable for R(free) tests (negative nrf), and since it requires much less memory than L.S. there will rarely be any reason to change maxvec from its default value. The CGLS algorithm is based closely on the procedure described by W.A. Hendrickson and J.H. Konnert (Computing in Crystallography, Ed. R. Diamond, S. Ramaseshan and K. Venkatesan, I.U.Cr. and Indian Academy of Sciences, Bangalore 1980, pp. 13.01-13.25). The structure-factor derivatives contribute only to the diagonal elements of the least-squares matrix, but all 'additional observational equations' (restraints) contribute in full to diagonal and off- diagonal terms, although neither the l.s. matrix A nor the Jacobean J are ever generated. The preconditioning recommended by Hendrickson and Konnert is used to speed up the convergence of the internal conjugate gradient iterations, and has the additional advantage of preventing the excessive damping of poorly determined parameters characteristic of other conjugate gradient algorithms (D.E. Tronrud, Acta Cryst. A48 (1992) 912-916). A further refinement in the CGLS approach is to save the parameter shifts from the previous full CGLS cycle, and to use them to estimate a shift multiplication factor independently for each parameter. This parameter is larger when a parameter appears to 'creep' in the same direction in successive cycles, and small when it oscillates. This technique significantly improves the convergence properties of the CGLS approach, because it indirectly takes into account the correlation terms which were ignored (to save time and space); however it cannot be used with BLOC or 'CGLS -nls'. The maximum and minimum shifts are set by the SLIM instruction; usually it will not be necessary to change them, but if a CGLS refinement appears to be unstable, both parameters should be reduced; in such a case it would be even better to track down and fix the cause of the instability, e.g. trying to refine a structure in the wrong space group! SLIM f1 [0.8] f2 [0.2] Maximum and minimum shift multiplication factors for CGLS refinement as described in the previous paragraph. These numbers have no effect on L.S. refinement, but for full-matrix refinement the program still reduces the shifts on parameters that appear to oscillate. BLOC n1 n2 atomnames If n1 or n2 are positive, the x, y and z parameters of the named atoms are refined in the corresponding cycle. If n1 or n2 are negative, the occupation and displacement parameters are refined in cycle. Not more than two such parameters may be specified on a single BLOC instruction, but the same atoms may be mentioned in any number of BLOC instructions. To refine both x, y and z as well as displacement parameters for an atom in the same block, n1 and n2 should specify the same cycle number, but with opposite signs. A BLOC instruction with no atom names refines all atoms in the specified cycles. The pattern of blocks is repeated after the maximum block number has been reached if the number of L.S. refinement cycles is larger than the maximum BLOC |n1| or |n2|. If a cycle number less than the maximum |n1| or |n2| is not mentioned in any BLOC instruction, it is treated as full-matrix. The overall scale, batch/twin scale factors, extinction coefficient, SWAT g parameter and free variables (if present) are refined in every block. Riding (hydrogen) atoms and atoms in rigid groups are included in the same blocks as the atoms on which they ride. For example, a polypeptide consisting of 30 residues (residue numbers 1..30 set by RESI instructions) could be refined efficiently as follows (all non-hydrogen atoms assumed anisotropic): BLOC 1 BLOC -2 N_1 > O_16 BLOC -3 N_14 > O_30 which would ensure 3 roughly equally sized blocks of about 800 parameters each and some overlap between the two anisotropic blocks to avoid problems where they join. The geometric parameters would refine in cycles 1,4,7 .. and the anisotropic displacement parameters in the remaining cycles. An alternative good blocking strategy would be to divide the structure into three overlapping blocks of xyz and Uij parameters, and to add a fourth cycle in which all xyz but no Uij values are refined (these four blocks would then also each contain about 800 parameters), i.e.: BLOC 1 -1 N_1 > O_11 BLOC 2 -2 N_10 > O_21 BLOC 3 -3 N_20 > O_30 BLOC 4 DAMP damp [1] limse [15] damp is usually left at the default value unless there is severe correlation, e.g. when trying to refine a pseudo-centrosymmetric structure, or refining with few data per parameter (e.g. from powder data). A value in the range 1-10000 might then be appropriate. The diagonal elements of the least-squares matrix are multiplied by (1+damp/1000) before inversion; this is a version of the Marquardt algorithm (J. Soc. Ind. Appl. Math., 11 (1963) 431-441). A side-effect of damping is that the standard deviations of poorly determined parameters will be artificially reduced; it is recommended that a final least- squares cycle be performed with little or no damping in order to improve these estimated standard deviations. Theoretically, damping only serves to improve the convergence properties of the refinement, and can be gradually reduced as the refinement converges; it should not influence the final parameter values. However in practice damping also deals effectively with rounding error problems in the (single-precision) least-squares matrix algebra, which can present problems when the number of parameters is large and/or restraints are used (especially when the latter have small esd's), and so it may not prove possible to lift the damping entirely even for a well converged refinement. If the maximum shift/esd (excluding the overall scale factor) is greater than limse, all the shifts are scaled down by the same numerical factor so that the maximum is equal to limse. If the maximum shift/esd is smaller than limse no action is taken. This helps to prevent excessive shifts in the early stages of refinement. WGHT a [0.1] b [0] c [0] d [0] e [0] f [.33333] The weighting scheme is defined as follows: w = q / [ sigma^2(Fo^2) + (a*P)^2 + b*P + d + e*sin(theta) ] where P = [ f * Maximum of(0 or Fo^2) + (1-f) * Fc^2 ]. It is possible for the experimental Fo^2 value to be negative because the background is higher than the peak; such negative values are replaced by 0 to avoid possibly dividing by a very small or even negative number in the expression for w. For twinned and powder data, the Fc^2 value used in the expression for P is the total calculated intensity obtained as a sum over all components. q is 1 when c is zero, exp[c*(sin(theta)/lambda)^2] when c is positive, and 1 - exp[c*(sin(theta)/lambda)^2] when c is negative. The use of P rather than (say) Fo^2 reduces statistical bias (A.J.C. Wilson, Acta Cryst., A32 (1976) 994-996). The weighting scheme is NOT refined if a is negative (contrast SHELX-76). The parameters can be set by trial and error so that the variance shows no marked systematic trends with the magnitude of Fc^2 or of resolution; the program suggests a suitable WGHT instruction after the analysis of variance. This scheme is chosen to give a flat analysis of variance in terms of Fc^2, but does not take the resolution dependence into account. It is usually advisable to retain default weights (WGHT 0.1) until all atoms have been found, when the scheme suggested by the program can be used for the next refinement job by replacing the WGHT instruction (if any) by the one output by the program towards the end of the .res file. This procedure is adequate for most routine refinements. It may be desirable to use a scheme which does not give a flat analysis of variance to emphasize particular features in the refinement; for example c = +10 or -10 would weight up data at higher 2-theta, e.g. to perform a 'high- angle' refinement (uncontaminated by hydrogen atoms which contribute little at higher diffraction angle) prior to a difference electron density synthesis (FMAP 2) to locate the hydrogens. The exponential weights which are obtained when c is positive were advocated by J.D. Dunitz and P. Seiler, Acta Cryst., B29 (1973) 589-595. Weighting up the high angle reflections will in general give X-ray atomic coordinates which are closer to those from neutron diffraction. Refinement against F^2 requires different weights to refinement against F; in particular, making all the weights equal ('unit weights'), although useful in the initial stages of refinement against F, is NEVER a sensible option for F^2. If the program suspects that an unsuitable WGHT instruction has been accidentally retained for a structure which had been refined previously with SHELX-76 or the XLS program in the Siemens SHELXTL system, it will output a warning message. FVAR osf [1] free variables The overall scale factor is followed by the values of the 'free variables' fv(2) ... The overall scale factor is given throughout as the square root of the scale factor which multiplies Fc^2 in the least-squares refinement [to make it similar to the scale factor in SHELX-76 which multiplied Fc], i.e. osf^2*Fc^2 is fitted to Fo^2. SHELXL-93 goes to some trouble to ensure that the initial value of the scale factor has very little influence. Firstly a quick structure factor summation with a small fraction of the total number of reflections is performed to estimate a new scale factor. If the values differ substantially then the new value is used. Secondly the scale factor is factored out of the least-squares algebra so that, although it is still refined, the only influence the previous value has is an indirect one via the weighting scheme and extinction correction. Before calculating electron density maps and the analysis of variance, and writing the structure factor file ('name.fcf'), the observed F^2 values and esd's are brought onto an absolute scale by dividing by the scale factor. The free variables allow extra constraints to be applied to the atoms, e.g. for common site occupation factors or isotropic displacement parameters, and may be used in conjunction with the SUMP, DFIX and CHIV restraints. If there is more than one FVAR instruction, they are concatenated; they may appear anywhere between UNIT and HKLF (or END). LISTS AND TABLES The esds in bond lengths, angles and torsion angles, chiral volumes, Ueq, and coefficients of least-squares planes and deviation of atoms from them, are estimated rigorously from the full correlation matrix (an approximate treatment is used for the angles between least-squares planes). The errors in the unit-cell dimensions (specified on the ZERR instruction) are taken into account exactly in estimating the esds in bond lengths, bond angles, torsion angles and chiral volumes. Correlation coefficients between the unit-cell dimensions are ignored except when determined by crystal symmetry (so that for a cubic crystal the cell esds contribute to errors in bond lengths and chiral volumes but not to the errors in bond angles or torsion angles). The (rather small) contributions of the unit-cell errors to the esds of quantities involving least-squares planes are estimated using an isotropic approximation. For full-matrix refinement, the esds are calculated after the final refinement cycle. In the case of BLOC'ed refinement, the esds are calculated after every cycle (except that esds in geometric parameters are not calculated after pure Uij/sof cycles etc.), and the maximum estimate of each esd is printed. This prevents some esds being underestimated because not all of the relevant atoms were refined in the last cycle, but at the cost of overestimating all the esds if the R-factor drops appreciably during the refinement. Thus large structures should first be refined almost to convergence (either by CGLS or L.S./BLOC), and then a separate final blocked refinement job performed to obtain the final parameters and their esds. It is important that there is sufficient overlap between the blocks to enable every esd to be estimated with all contributing atoms refining in at least one of the refinement cycles. BOND atomnames BOND outputs bond lengths for all bonds defined in the connectivity list which involve two atoms named on the same BOND instruction. Angles are output for all pairs of such bonds involving a common atom. Numerical parameters on a BOND instruction are ignored, but not treated as errors (for compatibility with SHELX-76). A BOND instruction with no parameters outputs bond lengths (and the corresponding angles) for ALL bonds in the connectivity table, and 'BOND $H' on its own includes all bonds to hydrogens as well (but - as usual - the hydrogens are not included in the connectivity table, so bonds involving symmetry equivalent hydrogens are not included). Other element names may also be referenced globally by preceding them with a '$' on a BOND instruction. BOND is set automatically by ACTA, and the bond lengths and angles are written to the .cif file. CONF atomnames The named atoms define a chain of at least four atoms. CONF generates a list of torsion angles with esd's for all torsion angles defined by this chain. CONF is often used to specify an n-membered ring, in which case the first three atoms must be named twice (n+3 names in all). If no atoms are specified, all possible torsion angles not involving hydrogen are generated from the connectivity array. The torsion angles generated by CONF are also written to the .cif file if an ACTA instruction is present. All torsion angles calculated by SHELXL-93 follow the conventions defined by F.H. Allen and D. Rogers, Acta Cryst., B25 (1969) 1326. MPLA na atomnames A least-squares mean plane is calculated through the first na of the named atoms, and the equation of the plane and the deviations of all the named atoms from the plane are listed with estimated standard deviations (from the full covariance matrix). The angle to the previous least-squares plane (if any) is also calculated, but some approximations are involved in estimating its esd. na must be at least 3. If na is omitted the plane is fitted to all the atoms specified. RTAB codename atomnames Chiral volumes (one atomname), bonds (two), angles (three) and torsion angles (four atomnames) are tabulated compactly against residue name and number. codename is used to identify the quantity being printed; it must begin with a letter and not be longer than 4 characters (e.g. 'Psi' or 'omeg'). There may not be more than 4 atom names. It is assumed that the atoms have the same names in all the required residues. For chiral volumes only, the necessary bonds must be present in the connectivity list (the same conventions are employed as for CHIV). Since the atoms do not themselves have to be in the same residue (it is sufficient that the names match), the residue name (if any) is printed as that of the first named atom for distances, the second for angles, and the third in the case of torsion angles. The latter should be consistent with generally accepted conventions for proteins. A typical application of RTAB for small-molecule structures is the tabulation of hydrogen-bonded distances and angles (with esd's) since these will not usually appear in the tables created automatically by BOND. If RTAB refers to more than one residue (e.g. RTAB_*), it is ignored for those residues in which not all the required atoms can be found (e.g. some of the main chain torsional angles for the terminal residues in a protein). LIST m [#] mult [1] m = 0: No action. m = 1: Write h,k,l, Fo, Fc and phase (in degrees) to .fcf in XPLOR format. Only unique reflections after removing systematic absences, scaling [to an absolute scale of F(calc)], applying dispersion and extinction or SWAT corrections (if any), and merging equivalents including Friedel opposites are included. If Fo^2 was negative, F(obs) is set to zero. Reflections suppressed by OMIT or SHEL [or reserved for R(free)] are not included. m = 2: Write h,k,l, Fo, sigma(Fo) and phase angle in degrees in FORMAT(3I4, 2F8.2,I4) for the reflection list as defined for m = 1. m = 3: Write h,k,l, Fo, sigma(Fo), A(real) and B(imag) in FORMAT(3I4,4F8.2), the reflections being processed exactly as for m = 1. m = 4: Write h,k,l, Fc^2, Fo^2, sigma(Fo^2) and a one-character status flag. Fo^2 are scaled to Fc^2 and possibly corrected for extinction, but no corrections have been made for dispersion and no further merging has been performed. FORMAT(3I4,2F12.2,F10.2,1X,A1) is employed. The status flag is 'o' (observed), 'x' [observed but suppressed using 'OMIT h k l', SHEL or reserved for R(free)], or '<' (Fo^2 is less than t.sigma(Fo^2), where t is one half of the F-threshold s specified on an OMIT instruction). m = 5: Write h,k,l, Fo, Fc, and phase in degrees in FORMAT(3I4,2F10.2,F7.2) for the reflection list as defined for m = 1. Like the m = 1 option, this is intended for input to standard macromolecular FFT programs (such as W. Furey's PHASES program), thereby providing a route to a graphical display of the electron density. For m = 4 only, mult is a constant multiplicative factor applied to all the quantities output (except the reflection indices!), and may be used if there are scaling problems. For other m options mult is ignored. For m = 2, 3 or 4 only a blank line is included at the end of the file as a terminator. The reflection list is written to the file 'name.fcf', which is in CIF format for n = 3 or 4; however the actual reflections are always in fixed format except for n = 1. The program CIFTAB can - amongst other options - read the m = 4 output and print Fo/Fc/sigma(F) tables in compact form on an HP-compatible laser-printer (see Appendix C). ACTA labelcode [1] A 'Crystallographic Information File' file 'name.cif' is created in self- defining STAR format. This ASCII file is suitable for data archiving, network transmission, and (with suitable additions) for direct submission for publication. ACTA automatically sets the BOND, FMAP 2, PLAN and LIST 4 instructions, and may not be used with other FMAP or LIST instructions or with a positive OMIT s threshold. A warning message appears if the cell contents on the UNIT instruction are not consistent with the atom list, because they are used to calculate the density etc. which appears in the '.cif' output file. If labelcode is set to one (or is absent) the atom labels in the cif file are generated assuming that typical small-molecule atom names have been used, i.e. CE1 is translated as Ce1, and if residue numbers are used they are appended directly, e.g. C2B_3; residue classes are not included in the atom labels. A labelcode of 2 implies that atoms have been named in a typical protein manner; CE1 in residue number 34 which is of class PHE generates the atom label C_E1_Phe_34. SIZE dx dy dz dx, dy and dz are the three principal dimensions of the crystal in mm, as usually quoted in publications. This information is written to the '.cif' file (and also used by SHELXA). TEMP T [20] Sets the temperature T of the data collection in degrees Celsius. This is reported to the .cif file and used to set the default isotropic U values for all atoms. TEMP must come before all atoms in the .ins file. TEMP also sets the default X-H bond lengths (see AFIX) which depend slightly on the temperature because of librational effects. The default C-H bond lengths and default U-values are rounded to two decimal places so that they may be quoted more easily. WPDB n [1] Writes the refined coordinates to a '.pdb' file. If n is positive hydrogen atoms are omitted; if |n| is 1 all atoms are converted to isotropic and ATOM statements generated, and if |n| is 2 ANISOU statements are also generated (but the equivalent B value is still used on the ATOM statement). The atom names and residue classes and numbers should conform to PDB conventions. This provides a direct link to XPLOR and other programs which use the official (Brookhaven) dialect of the PDB format. Note however that XPLOR requires that solvent (water) atoms are each placed in a separate residue; this is not standard PDB format and is not generated by SHELXL-93. FOURIER, PEAK SEARCH AND LINE PRINTER PLOTS FMAP code [2] axis [#] nl [53] The unique unit of the cell for performing the Fourier calculation is set up automatically unless specified by the user using FMAP and GRID; the value of axis must be non-zero to suppress the automatic selection. The program chooses a 53 x 53 x nl or 103 x 103 x nl grid depending on the resolution of the data. axis is 1, 2 or 3 to define the direction perpendicular to the layers. Dispersion corrections are applied (so that the resulting electron density is real) and Friedel opposites are merged after the least-squares refinement and analysis of variance but before calculating the Fourier synthesis. This will improve the map (and bring the maximum and minimum residual density closer to zero) compared with SHELX-76. In addition, since usually all the data are employed, reflections with sigma(F) relatively large compared with Fc are weighted down. This should be better than the use of an arbitrary cutoff on Fo/sigma(F). The rms fluctuation of the map relative to the mean density is also calculated; in the case of a difference map this gives an estimate of the 'noise level' and so may be used to decide whether individual peaks are significant. If code is made negative, both positive and negative peaks are included in the list, sorted on the absolute value of the peak height. This is intended to be useful for neutron diffraction data. code = 2: Difference electron density synthesis with coefficients (Fo-Fc) and phases phi(calc). code = 3: Electron density synthesis with coefficients Fo and phases phi(calc). code = 4: Electron density synthesis with coefficients (2Fo-Fc) and phases phi(calc). F(000) is included in the Fourier summations for code = 3 and 4. GRID sl [#] sa [#] sd [#] dl [#] da [#] dd [#] Fourier grid, when not set automatically. Starting points and increments multiplied by 100. s means starting value, d increment, l is the direction perpendicular to the layers, a is across the paper from left to right, and d is down the paper from top to bottom. Note that the grid is 53 x 53 x nl points, i.e. twice as large as in SHELX-76, and that sl and dl need not be integral. The 103 x 103 x nl grid is only available when it is set automatically by the program (see above). PLAN npeaks [20] d1 [#] d2 [#] If npeaks is positive a Fourier peak list is printed and written to the .res file; if it is negative molecule assembly and line printer plots are also performed. For negative npeaks, distances involving peaks which are less than r1+r2+d1 (the covalent radii r are defined via SFAC; 1 and 2 refer to the two atoms concerned) are printed and used to define 'molecules' for the line printer plots. Distances involving atoms and/or peaks which are less than r1+r2+|d2| are considered to be 'non-bonded interactions'; however distances in which both atoms are hydrogen or at least one is carbon (recognised by SFAC label 'C') are ignored. The default values of d1 and d2 (for negative npeaks) are 0.5 and 2.0 resp. These non-bonded interactions are ignored when defining molecules, but the corresponding atoms and distances are included in the line printer output. Thus an atom or peak may appear in more than one map, or more than once on the same map. A table of the appropriate coordinates and symmetry transformations appears at the end of each molecule. Negative d2 includes hydrogen atoms in the line printer plots, otherwise they are left out (but included in the distance tables). For the purposes of the PLAN instruction, a hydrogen atom is one with a radius of less than 0.4 Angstrom. Peaks are assigned the radius of SFAC type 1, which is usually set to carbon. Peaks appear on the printout as numbers, but in the .res file they are given names beginning with 'Q' and followed by the same numbers. Since only three digits are available for the number, the absolute value of npeaks may not exceed 999. Peak heights are also written to the .res file (after the sof and dummy U values) in electrons per cubic Angstrom. See also MOLE for forcing molecules (and their environments) to be printed separately. A default npeaks of +20 is set by FMAP; to obtain line printer plots, an explicit PLAN instruction with negative npeaks is required. If npeaks is positive the nearest unique atoms to each peak are tabulated, together with the corresponding distances. A table of shortest distances between peaks is also produced. If npeaks is positive d1 and d2 have a different meaning. The default of d1 is then -1 and causes the full peaklist to appear in the .res file. If it is positive (say 2.3) then the full peaklist is still printed in the .lst file, but only suitable candidates for (full occupancy) water molecules appear in the .res file (with SFAC 4 and U set to 0.75). The water molecules must be less than 4 Angstroms from an atom which begins with 'O', 'N' or 'W', and may not be less than d2 (default 3.0) from any atom which does not begin with 'O', 'N', 'W' or 'H', and may not be nearer than d1 to any 'O', 'N' or 'W' atom or potential waters which have larger peak heights. This facility is intended for extending the water structure of proteins in connection with BUMP and SWAT. To include the waters in the next refinement job, their names need to be changed and they need to be moved to before the HKLF instruction at the end of the atom list in the new .ins file. It is recommended that the last water is called 'LAST' on the ISOR and CONF instructions so that this name does not need to be updated each job. MOLE n Forces the following atoms, and atoms or peaks that are bonded to them, into molecule n of the PLAN output. n may not be greater than 99. n = 99 has a special meaning: the 'line printer plot' is suppressed for the following atoms, but the table of distances is still printed. This is sometimes useful for saving paper, e.g. for solvent water in protein structures. FURTHER INFORMATION The author may be contacted via email ( gsheldr @ ibm.gwdg.de ) or fax (Germany [from the US 01149-, from the UK 01049- and from most other countries 0049-] -551-393373). He would be particularly interested to hear of any problems in the installation and use of the program and of any errors or lack of clarity in this instruction summary. A satirical description of the SHELX programming philosophy may be found in Current Contents (Physical, Chemical and Earth Sciences), Vol. 29, Number 41 (1989) page 14. The task of writing this program was made considerably easier by the incorporation of many ideas and algorithms proposed by Durward Cruickshank, Howard Flack, Wayne Hendrickson, John Konnert, John Rollett, Dieter Schwarzenbach and David Watkin, that had already been tested by these authors in their own excellent programs. Ward Robinson proved invaluable in making the documentation comprehensible. My research group in Goettingen had no choice but to suffer the 'alpha-test', and ca. 100 colleagues at different institutions around the world provided invaluable feedback in the 'beta-' and 'gamma-tests'. Syd Hall was most helpful and persuasive in the implementation of CIF format. The IUCr kindly gave permission for scattering factors, absorption coefficients etc. from the new Volume C of International Tables to be used prior to publication, and should also have the final word of caution: "Thoughtless use of established procedures in widely distributed software may be as harmful as the natural tendency of most people to prefer results in agreement with preconceived ideas", D. Schwarzenbach et al., Report of the IUCr Subcommittee on Statistical Descriptors, Acta Cryst., A45 (1989) 63-75. George Sheldrick Appendix A - Absorption corrections with SHELXA-92 -------------------------------------------------- SHELXA-93 is currently under development. Licensed users of SHELXL-93 will be informed when it is ready for release. Appendix B - PDB to '.ins' format conversion with PDBINS -------------------------------------------------------- The auxiliary program PDBINS reads a PDB format file and writes a '.ins' file for SHELXL-93. There are no command line options and the program runs interactively, asking the user to supply missing information. It is assumed that the PDB file conforms to the specifications in the PDB documentation 'Atomic Coordinate and Bibliographic Entry Format Description' of Feb. 1992. Atom lists from XPLOR and some other programs can be read, but if the conventions for transforming from orthogonal to crystallographic coordinates do not correspond to those in the above document, then appropriate SCALEn records must precede the ATOM or HETATM records. Note that SHELXL-93, unlike XPLOR, does not allow the same residue number to be used with different residue classes, and that the SHELXL-93 residue classes must begin with a letter and the SHELXL-93 residue numbers must be pure numbers and may not contain non-digits. XPLOR usually requires each solvent molecule to be defined as a separate residue, whereas for SHELXL-93 the solvent may either be treated in this way or assigned to the (default) residue number zero. PDBINS may renumber the residues if the current numbering scheme would be inconvenient for SHELXL-93. If there is more than one chain (or molecule) in the asymmetric unit, different residue numbers are required and there should be a gap of one or more residue numbers between different chains (otherwise there are problems with C_- and N_+ etc.). PDBINS reads restraints and other standard instructions from a residue dictionary file 'shelxl.dic'. Users are encouraged to use this file as a model for their own dictionary files (which should be given different names). If the protein contains disordered or non-standard residues, some editing of the resulting '.ins' file will be required before SHELXL-93 can be run. The order of atoms in each residue is irrelevant for SHELXL-93, but for PDBINS there are advantages in putting the atom named 'N' (the peptide nitrogen) first in each residue (as is normal practice). Some restraints may be missing if non-standard residue or atom names are used; note that PDBINS expects the C-terminal oxygen to be called OXT and not to be put in a separate residue. PDBINS converts OT to OXT for the C-terminus and CD to CD1 in isoleucine in accordance with PDB rules. In addition, PDBINS generates restraints for disulfide bridges linking residues CYS (or CSS). PDBINS uses the first character of the atom name as the element name, and recognizes two character element names if they start one column to the left, in accordance with PDB rules. SHELXL-93 may be run with Friedel opposites NOT averaged (in which case no MERG instruction is needed; this is the correct option when significant anomalous scatterers e.g. iron (using CuKa) are present) or using MERG 4 to average Friedel opposites and set the dispersion terms f" to zero. Note that XPLOR and many other macromolecular programs, unlike SHELXL-93, require a reflection list in which Friedel opposites have already been merged. PDBINS creates a '.pdl' file which gives residue names and compositions and other useful information; this file should be printed out and retained for reference during the refinement. PDBINS is written in essentially machine independent FORTRAN-77. Before compiling it the comments in the source should be consulted and the following three changes may be required: (a) it is advisable to open the .ins and .pdl files with CARRIAGECONTROL='LIST' for VAX/VMS systems, (b) the only format statement in subroutine GETANS may be changed to end with ',$' to tidy up the console output for VAX/VMS and some other systems and (c) the variable CR may be set to CHAR(13) in the first executable statement in the main program if the program is to run on a UNIX machine which shares a disk with MSDOS machines using NFS network software. This enables DOS programs such as the Siemens SHELXTL-PC system to read the files directly. For pure UNIX AND VMS systems CR should be set to CHAR(32). Appendix C - Tables production from .'cif' and '.fcf' files using CIFTAB ------------------------------------------------------------------------ The auxiliary program CIFTAB is provided with SHELXL-93 to facilitate the transition to CIF. In contrast to the actual SHELX programs, the FORTRAN code is not intended to be treated as sacrosanct; it may be modified and extended by users as the need arises. CIFTAB should be run interactively from a console; there are no command line options. The program is available as an essentially computer independent FORTRAN-77 source, or in precompiled form for certain hardware configurations. Before compiling it on a new system the comments in the source should be consulted (see also the last paragraph of the PDBINS description immediately above). CIFTAB reads a '.cif' or '.fcf' file written by SHELXL-93 and provides the following facilities, which may be selected from a menu: 1. Some of the items which are unknown to SHELXL-93 and so are present as '?' in the .cif file may be replaced by the corresponding items from other CIF files, written for example by diffractometer control, data reduction or absorption correction programs. Only non-looped '?' items are resolved in this way. 2. Structure factor tables may be output in compressed form on HP-Laserjet compatible printers (or to file in the corresponding format for network transmission to such a printer). 3. Tables of crystal data, atom parameters, bond lengths and angles, anisotropic displacement parameters and hydrogen atom coordinates may be produced in a format specified in a file 'ciftab.???' (where ??? is any three letter combination). A standard ASCII file 'ciftab.def' is provided; users may use it as a model for preparing files to conform with the various journal requirements etc. This means that it is not necessary to modify and recompile the program each time a journal changes its rules. Extra files are provided for users of the Siemens SHELXTL system which produce '.tex' files for printing via the Siemens XTEXT program; this includes the production of tables in German and provides much more flexibility in the handling of Greek and other special characters. The format file is simply copied to the output file, except that directives (lines beginning with '?' or '$') have a special meaning, '\n\' (where n is a number) is replaced by the ASCII character n (e.g. \12\ starts a new page), and CIF identifiers (which begin with the character '_') are replaced by the appropriate number or string from the CIF file. CIF identifiers may optionally be followed (without an intervening space) by one or more of: 'n', ':n' and '=n' where n is an integer; the CIF identifier (including qualifier) must be terminated by one space, which is not copied to the output file. 'n' right justifies a string or justifies a number so that the figure immediately to the left of the decimal point appears in column n; if there is no decimal point then the last digit appears in column n. In either case the standard deviation (if any) extends to the right with brackets but without intervening spaces. If 'n' are both absent, the CIF item is inserted at the current position. If ':n' is absent the item is treated as a string (see above), otherwise it is treated as a number; n is the power of 10 with which the CIF item should be multiplied, and is useful for converting Angstroms to pm or printing coordinates as integers; n may be negative, zero or positive. '=n' rounds the CIF item (after application of ':n') so that there are not more than n figures after the decimal point; n must be zero or positive. A line beginning with 'loop_' is repeated until the corresponding loop in the CIF file is exhausted; all the CIF items in the line must be in the same loop in the CIF input file. All CIF data names and the string 'loop_' must be given as lower case in the format file; in the CIF input file the standard CIF rules apply. A line containing at least 4 consecutive underscores is copied to the output file unchanged, and may be used for drawing a horizontal line. There are also two pseudo-CIF-identifies: '_tabno' is the number of the table, and '_comno' is a number to identify the compound. Both may be set via the CIFTAB menu. '_tabno' but not '_comno' is incremented each time it is used. An underscore '_' followed by a space may be used to continue on the next line without creating a new line in the output file. Lines beginning with question marks are output to the console (without the leading question mark) as questions; if the answer to the question is not 'Y' or 'y', everything in the format file is skipped until the next line which begins with a question mark. Lines beginning with a dollar '$' are not interpreted as text, but are scanned for the following strings (upper or lower case, quotes not essential): 'xtext': output should be formatted for the Siemens SHELXTL xtext program. 'xtext,deutsch': as above, but translated into German. The above directive, if present, should be the first line of the format file. The directive $symops:n, where n is an integer, prints the symmetry operations used to generate equivalent atoms, starting each line of text in column n. These operators are references by '#m' (where m is an integer) after the atom name. The line beginning '$symops:n' usually follows the table of selected bond lengths and angles, but could also be used for a torsion angles table. The remaining directives may appear at any point in the format file except immediately after a continuation line marker, but always on a line beginning with '$'. 'h=none': leave out all hydrogen atoms. 'h=only': leave out all non-hydrogen atoms. 'h=free': leave out riding or rigid group hydrogens but include the rest. 'h=all': include all hydrogen and all other atoms. The hydrogen atom directives apply only to coordinates tables; hydrogen atoms are recognised by the .._type_symbol 'H'. The publication flags can be used to control which hydrogen atoms appear in tables of bond lengths, angles etc. 'brack': Atom names should include brackets (if present in the CIF file). 'nobrack': Brackets are deleted from the atom names. 'flag': Only output items for which the publication flag is 'Y' or 'y'. 'noflag': Output all items, ignoring the publication flag. The default settings are '$h=none,brack,flag'. The standard tables file 'ciftab.def' illustrates the use of most of these facilities. CIFTAB extends some of the standard CIF codes to make them more suitable for tables, and also takes special action when items such as _refine_ls_extinction_coef are missing or undefined. Appendix D - Example of an Acta Cryst. paper in '.cif' format ------------------------------------------------------------- The following example is based on a paper submitted to Acta Crystallographica in CIF format; it has been edited slightly since submission. data_global #============================================================================ # 1. SUBMISSION DETAILS _publ_contact_author # Name and address of author for correspondence ; Ehmke Pohl Institut f\"ur Anorganische Chemie Universit\"at G\"ottingen Tammannstr. 4 3400 G\"ottingen Bundesrepublik Deutschland ; _publ_contact_author_phone '049 551 393075' _publ_contact_author_fax '049 551 393373' _publ_contact_author_email epohl@ibm.gwdg.de _publ_requested_journal 'Acta Crystallographica C' _publ_requested_coeditor_name ? _publ_contact_letter ; Please consider this CIF submission for publication as a Regular Structure Paper in Acta Crystallographica C. ; #============================================================================ # 2. PROCESSING SUMMARY (IUCr Office Use Only) _journal_date_recd_electronic ? _journal_date_to_coeditor ? _journal_date_from_coeditor ? _journal_date_accepted ? _journal_date_printers_first ? _journal_date_printers_final ? _journal_date_proofs_out ? _journal_date_proofs_in ? _journal_coeditor_name ? _journal_coeditor_code ? _journal_coeditor_notes ? _journal_techeditor_code ? _journal_techeditor_notes ? _journal_coden_ASTM ? _journal_name_full ? _journal_year ? _journal_volume ? _journal_issue ? _journal_page_first ? _journal_page_last ? _journal_suppl_publ_number ? _journal_suppl_publ_pages ? #============================================================================ # 3. TITLE AND AUTHOR LIST _publ_section_title ; Structures of Aminotriphenylphosphonium Bromide and Hexachloroantimonate ; # The loop structure below should contain the names and addresses of all # authors, in the required order of publication. Repeat as necessary. loop_ _publ_author_name _publ_author_address 'Pohl, Ehmke' ; Institut f\"ur Anorganische Chemie Universit\"at G\"ottingen Tammannstr. 4 3400 G\"ottingen Bundesrepublik Deutschland ; 'Gosink, Hans J.' ; Institut f\"ur Anorganische Chemie Universit\"at G\"ottingen Tammannstr. 4 3400 G\"ottingen Bundesrepublik Deutschland ; 'Herbst-Irmer, Regine' ; Institut f\"ur Anorganische Chemie Universit\"at G\"ottingen Tammannstr. 4 3400 G\"ottingen Bundesrepublik Deutschland ; 'Noltemeyer, Mathias' ; Institut f\"ur Anorganische Chemie Universit\"at G\"ottingen Tammannstr. 4 3400 G\"ottingen Bundesrepublik Deutschland ; 'Roesky, Herbert W.' ; Institut f\"ur Anorganische Chemie Universit\"at G\"ottingen Tammannstr. 4 3400 G\"ottingen Bundesrepublik Deutschland ; 'Sheldrick, George M.' ; Institut f\"ur Anorganische Chemie Universit\"at G\"ottingen Tammannstr. 4 3400 G\"ottingen Bundesrepublik Deutschland ; #============================================================================ # 4. TEXT _publ_section_abstract ; The structures of aminotriphenylphosphonium bromide and hexachloroantimonate are stabilized by hydrogen bonds. ; _publ_section_comment ; The aminotriphenylphosphonium bromide (I) and hexachloroantimonate (II) have been structurally characterized. There are two formula units of (II) in the asymmetric unit. Both compounds form hydrogen bonds from the amino hydrogen atoms to the anions. The positions of the amino hydrogen atoms were refined with distance restraints for the N-H distances. The N-Br distances in I are 3.310(2) and 3.373 (2) \%A, the N-Cl distances in II are 3.594 (4), 3.563(4), 3.740(5) and 3.537(5) \%A. All other distances and angles are generally as expected. They correspond well with values found in the aminotriphenylphosphonium chloride (Hursthouse, Walker, Warrens @ Woolins, 1985), the aminotriphenylphosphonium (1,2,-bis(benzamid-2'-olato)phenyl- N,N',O,O')nitrido osmium (IV) (Barner, Collins, Maper and Santasiero, 1986) and the amino triphenylphosphonium (di(thiazane)-3-eno-N,S)-thiosulfato- triphenyl-phosphine platinum (Hursthouse, Short, Kelly @ Woolins, 1988). ; _publ_section_experimental ; Data were collected by the real-time learnt profile method (Clegg, 1981). Scattering factors, dispersion corrections and absorption coefficients were taken from International Tables for Crystallography, Vol. C. (1992), tables 6.1.1.4, 4.2.6.8 and 4.2.4.2 respectively. Since I crystallizes in a polar space group, polar axis restraints were applied by the method of Flack @ Schwarzenbach (1988) and the absolute structure of the crystal used for the investigation was established as described by Flack (1983). ; _publ_section_references ; Barner, J.C., Collins, T.J., Mapes, B.E. @ Santasiero, B.D. (1986). Inorg. Chem. 25, 4322-4323. Clegg, W. (1981). Acta Cryst. A37, 22-28. Flack, H.D. (1983). Acta Cryst. A39, 876-881. Flack, H.D. @ Schwarzenbach, D. (1988). Acta Cryst. A44, 499-506. Hursthouse, M.B., Short, R.L., Kelly, P.F. @ Woollins, J.D. (1988). Acta Cryst. C44, 1731-1733. Hursthouse, M.B., Walker, N.P.C., Warrens, C.P. @ Woollins, J.D. (1985). J. Chem. Soc., Dalton Trans., 1043-1047. International Tables for Crystallography (1992). Vol. C. Dordrecht: Kluwer Academic Publishers. Sheldrick, G.M. (1990). Acta Cryst. A46, 467-473. Sheldrick, G.M. (1993). In preparation for J. Appl. Cryst. ; _publ_section_figure_captions ; Fig.1 : Structure of I showing 50 % probability displacement ellipsoids The hydrogen atoms are omitted for clarity. Fig.2 : Structure of II showing 50 % probability displacement ellipsoids. The hydrogen atoms are omitted for clarity. ; _publ_section_acknowledgements ; This work was supported by the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie. ; #============================================================================ data_alge _audit_creation_method SHELXL _chemical_name_systematic ; Amino(triphenyl)phosphonium Bromide ; _chemical_name_common ? _chemical_formula_moiety ? _chemical_formula_structural ? _chemical_formula_analytical ? _chemical_formula_sum 'C18 H17 Br N P' _chemical_formula_weight 358.21 _chemical_melting_point ? _chemical_compound_source ? loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source 'C' 'C' 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'H' 'H' 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'P' 'P' 0.1023 0.0942 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'N' 'N' 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'Br' 'Br' -0.2901 2.4595 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Orthorhombic _symmetry_space_group_name_H-M Pna2(1) loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, -y, z+1/2' 'x+1/2, -y+1/2, z' '-x+1/2, y+1/2, z+1/2' _cell_length_a 10.978(2) _cell_length_b 9.628(2) _cell_length_c 15.530(3) _cell_angle_alpha 90.00 _cell_angle_beta 90.00 _cell_angle_gamma 90.00 _cell_volume 1641.5(3) _cell_formula_units_Z 4 _cell_measurement_temperature 153(2) _cell_measurement_reflns_used 56 _cell_measurement_theta_min 10 _cell_measurement_theta_max 12.5 _exptl_crystal_description 'Transparent blocks' _exptl_crystal_colour Colourless _exptl_crystal_size_max 0.4 _exptl_crystal_size_mid 0.2 _exptl_crystal_size_min 0.2 _exptl_crystal_density_meas ? _exptl_crystal_density_diffrn 1.449 _exptl_crystal_density_method ? _exptl_crystal_F_000 728 _exptl_absorpt_coefficient_mu 2.595 _exptl_absorpt_correction_type empirical _exptl_absorpt_correction_T_min 0.783 _exptl_absorpt_correction_T_max 0.952 _exptl_special_details ; ? ; _diffrn_ambient_temperature 153(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device 'Stoe-Siemens AED 4-circle-diffractometer' _diffrn_measurement_method 'Profile fitted 2\q/\w scans (Clegg, 1981)' _diffrn_standards_number 3 _diffrn_standards_interval_count ? _diffrn_standards_interval_time 90 _diffrn_standards_decay_% 0 _diffrn_reflns_number 3776 _diffrn_reflns_av_R_equivalents 0.0068 _diffrn_reflns_av_sigmaI/netI 0.0196 _diffrn_reflns_limit_h_min -15 _diffrn_reflns_limit_h_max 15 _diffrn_reflns_limit_k_min -11 _diffrn_reflns_limit_k_max 13 _diffrn_reflns_limit_l_min -21 _diffrn_reflns_limit_l_max 21 _diffrn_reflns_theta_min 4.23 _diffrn_reflns_theta_max 29.98 _reflns_number_total 3704 _reflns_number_observed 3385 _reflns_observed_criterion >2sigma(I) _computing_data_collection 'Stoe DIF4' _computing_cell_refinement 'Stoe DIF4' _computing_data_reduction 'Stoe REDU4' _computing_structure_solution 'SHELXS-86 (Sheldrick, 1990)' _computing_structure_refinement 'SHELXL-93 (Sheldrick, 1993)' _computing_molecular_graphics SHELXTL-Plus _computing_publication_material SHELXL-93 _refine_special_details ; Refinement on F^2^ for ALL reflections except for 3 with very negative F^2^ or flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The observed criterion of F^2^ > 2sigma(F^2^) is used only for calculating _R_factor_obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme 'calc w=1/[s^2^(Fo^2^)+( 0.0241P)^2^+0.6395P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary 'heavy-atom method' _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_extinction_method SHELXL-93 _refine_ls_extinction_expression 'Fc^*^=kFc[1+0.001xFc^2^l^3^/sin(2q)]^-1/4^' _refine_ls_extinction_coef 0.0050(3) _refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881' _refine_ls_abs_structure_Flack -0.016(7) _refine_ls_number_reflns 3701 _refine_ls_number_parameters 216 _refine_ls_number_restraints 106 _refine_ls_R_factor_all 0.0327 _refine_ls_R_factor_obs 0.0258 _refine_ls_wR_factor_all 0.0598 _refine_ls_wR_factor_obs 0.0547 _refine_ls_goodness_of_fit_all 1.102 _refine_ls_goodness_of_fit_obs 1.066 _refine_ls_restrained_S_all 1.095 _refine_ls_restrained_S_obs 1.049 _refine_ls_shift/esd_max 0.001 _refine_ls_shift/esd_mean 0.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_thermal_displace_type _atom_site_occupancy _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_group Br1 Br 0.38157(2) 0.27359(2) 0.50000(2) 0.02694(9) Uani 1 d . . P1 P 0.14371(4) 0.49898(7) 0.65684(4) 0.0173(2) Uani 1 d . . N1 N 0.1273(2) 0.3578(2) 0.60192(13) 0.0234(8) Uani 1 d D . H1A H 0.1853(23) 0.3285(33) 0.5715(17) 0.031(6) Uiso 1 d D . H1B H 0.0581(20) 0.3392(33) 0.5819(18) 0.031(6) Uiso 1 d D . C11 C 0.1653(2) 0.6551(2) 0.59526(13) 0.0209(9) Uani 1 d . . C12 C 0.2659(2) 0.6611(3) 0.5394(2) 0.0295(11) Uani 1 d D . H12 H 0.3171(6) 0.5838(9) 0.5328(2) 0.036(4) Uiso 1 calc RD . C13 C 0.2886(2) 0.7828(3) 0.4941(2) 0.0374(11) Uani 1 d D . H13 H 0.3568(8) 0.7880(3) 0.4576(5) 0.039(4) Uiso 1 calc RD . C14 C 0.2121(2) 0.8966(3) 0.5018(2) 0.0356(12) Uani 1 d D . H14 H 0.2281(3) 0.9781(10) 0.4706(4) 0.039(5) Uiso 1 calc RD . C15 C 0.1116(2) 0.8897(3) 0.5560(2) 0.0346(12) Uani 1 d D . H15 H 0.0591(7) 0.9666(9) 0.5612(2) 0.039(4) Uiso 1 calc RD . C16 C 0.0882(2) 0.7688(3) 0.6029(2) 0.0282(10) Uani 1 d D . H16 H 0.0203(8) 0.7644(3) 0.6396(4) 0.036(4) Uiso 1 calc RD . C21 C 0.0109(2) 0.5193(2) 0.72264(13) 0.0191(9) Uani 1 d . . C22 C 0.0224(2) 0.5529(3) 0.8098(2) 0.0261(10) Uani 1 d D . H22 H 0.0997(9) 0.5658(3) 0.8342(3) 0.036(4) Uiso 1 calc RD . C23 C -0.0819(2) 0.5672(3) 0.8600(2) 0.0336(12) Uani 1 d D . H23 H -0.0748(3) 0.5898(4) 0.9186(7) 0.039(4) Uiso 1 calc RD . C24 C -0.1958(2) 0.5483(3) 0.8241(2) 0.0303(11) Uani 1 d D . H24 H -0.2660(8) 0.5578(3) 0.8586(4) 0.039(5) Uiso 1 calc RD . C25 C -0.2077(2) 0.5154(3) 0.7374(2) 0.0253(9) Uani 1 d D . H25 H -0.2856(9) 0.5026(3) 0.7134(3) 0.039(4) Uiso 1 calc RD . C26 C -0.1045(2) 0.5011(3) 0.68582(14) 0.0210(9) Uani 1 d D . H26 H -0.1122(2) 0.4796(4) 0.6272(7) 0.036(4) Uiso 1 calc RD . C31 C 0.2764(2) 0.4780(2) 0.72269(13) 0.0187(9) Uani 1 d . . C32 C 0.3141(2) 0.3456(3) 0.7437(2) 0.0314(13) Uani 1 d D . H32 H 0.2720(5) 0.2682(9) 0.7220(3) 0.036(4) Uiso 1 calc RD . C33 C 0.4146(3) 0.3265(3) 0.7973(2) 0.0390(15) Uani 1 d D . H33 H 0.4408(4) 0.2364(11) 0.8113(2) 0.039(4) Uiso 1 calc RD . C34 C 0.4753(2) 0.4401(3) 0.8297(2) 0.0291(10) Uani 1 d D . H34 H 0.5433(8) 0.4270(3) 0.8658(4) 0.039(5) Uiso 1 calc RD . C35 C 0.4378(2) 0.5722(3) 0.8101(2) 0.0351(13) Uani 1 d D . H35 H 0.4788(5) 0.6489(9) 0.8335(3) 0.039(4) Uiso 1 calc RD . C36 C 0.3386(2) 0.5924(3) 0.7553(2) 0.0294(11) Uani 1 d D . H36 H 0.3139(4) 0.6829(11) 0.7406(2) 0.036(4) Uiso 1 calc RD . loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 Br1 0.02225(9) 0.03460(11) 0.02397(9) 0.00572(14) 0.00420(11) 0.01067(9) P1 0.0154(2) 0.0186(2) 0.0178(2) -0.0018(2) -0.0004(2) 0.0001(2) N1 0.0170(8) 0.0269(10) 0.0264(9) -0.0103(8) 0.0014(7) -0.0005(7) C11 0.0196(9) 0.0230(11) 0.0202(9) 0.0008(8) -0.0029(8) -0.0008(8) C12 0.0285(11) 0.0312(14) 0.0289(11) 0.0012(10) 0.0048(9) 0.0008(10) C13 0.0365(11) 0.0443(14) 0.0314(13) 0.011(2) 0.0016(13) -0.0098(11) C14 0.0403(12) 0.0326(12) 0.0339(11) 0.014(2) -0.0132(13) -0.0100(10) C15 0.0338(12) 0.0251(13) 0.0450(14) 0.0077(11) -0.0121(11) 0.0006(11) C16 0.0240(10) 0.0287(12) 0.0318(11) 0.0037(10) -0.0030(9) 0.0024(10) C21 0.0184(9) 0.0183(11) 0.0205(9) -0.0031(8) 0.0008(7) -0.0005(8) C22 0.0243(10) 0.0307(12) 0.0233(10) -0.0080(10) 0.0023(8) -0.0069(10) C23 0.0345(12) 0.039(2) 0.0279(12) -0.0154(11) 0.0076(10) -0.0094(12) C24 0.0259(11) 0.0293(13) 0.0356(13) -0.0099(11) 0.0126(10) -0.0038(10) C25 0.0183(9) 0.0230(12) 0.0346(12) -0.0022(10) 0.0039(8) -0.0010(8) C26 0.0207(9) 0.0215(10) 0.0209(9) -0.0020(8) 0.0000(7) 0.0017(8) C31 0.0178(9) 0.0201(10) 0.0182(9) 0.0001(8) 0.0003(7) -0.0003(7) C32 0.0387(13) 0.0204(12) 0.0350(12) -0.0046(10) -0.0143(10) 0.0049(10) C33 0.0459(15) 0.0287(14) 0.0423(15) -0.0028(12) -0.0163(13) 0.0132(13) C34 0.0220(10) 0.0391(14) 0.0263(11) 0.0047(10) -0.0069(8) 0.0012(10) C35 0.0332(13) 0.0320(14) 0.0401(13) 0.0080(12) -0.0153(11) -0.0125(11) C36 0.0318(11) 0.0200(11) 0.0364(12) 0.0042(10) -0.0125(10) -0.0072(10) _geom_special_details ; All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. Hydrogen bond details: H1A..BR1 2.481(22) N1..BR1 3.310(2) N-H1A..BR1 168(3) H1B..BR1' 2.560(23) N1..BR1' 3.373(2) N1-H1B..BR1' 163(3) ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag P1 N1 1.615(2) . yes P1 C21 1.791(2) . yes P1 C31 1.791(2) . yes P1 C11 1.797(2) . yes N1 H1A 0.84(2) . yes N1 H1B 0.84(2) . yes C11 C16 1.388(4) . ? C11 C12 1.406(3) . ? C12 C13 1.389(4) . ? C12 H12 0.939(11) . ? C13 C14 1.385(4) . ? C13 H13 0.941(11) . ? C14 C15 1.389(4) . ? C14 H14 0.939(11) . ? C15 C16 1.397(4) . ? C15 H15 0.942(11) . ? C16 H16 0.940(11) . ? C21 C22 1.397(3) . ? C21 C26 1.401(3) . ? C22 C23 1.392(3) . ? C22 H22 0.937(11) . ? C23 C24 1.381(4) . ? C23 H23 0.939(11) . ? C24 C25 1.389(3) . ? C24 H24 0.943(11) . ? C25 C26 1.395(3) . ? C25 H25 0.940(11) . ? C26 H26 0.937(11) . ? C31 C32 1.380(3) . ? C31 C36 1.392(3) . ? C32 C33 1.394(3) . ? C32 H32 0.939(11) . ? C33 C34 1.376(4) . ? C33 H33 0.939(11) . ? C34 C35 1.371(4) . ? C34 H34 0.942(11) . ? C35 C36 1.396(3) . ? C35 H35 0.938(11) . ? C36 H36 0.941(11) . ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag N1 P1 C21 107.58(10) . . yes N1 P1 C31 107.31(10) . . yes C21 P1 C31 110.39(10) . . yes N1 P1 C11 115.96(11) . . yes C21 P1 C11 108.64(11) . . yes C31 P1 C11 106.93(10) . . yes P1 N1 H1A 120(2) . . yes P1 N1 H1B 118(2) . . yes H1A N1 H1B 114(3) . . yes C16 C11 C12 119.9(2) . . ? C16 C11 P1 122.3(2) . . ? C12 C11 P1 117.8(2) . . ? C13 C12 C11 119.2(3) . . ? C13 C12 H12 120.4(2) . . ? C11 C12 H12 120.38(15) . . ? C14 C13 C12 120.9(3) . . ? C14 C13 H13 119.5(2) . . ? C12 C13 H13 119.5(2) . . ? C13 C14 C15 119.8(3) . . ? C13 C14 H14 120.1(2) . . ? C15 C14 H14 120.1(2) . . ? C14 C15 C16 120.1(3) . . ? C14 C15 H15 120.0(2) . . ? C16 C15 H15 120.0(2) . . ? C11 C16 C15 120.1(2) . . ? C11 C16 H16 119.96(14) . . ? C15 C16 H16 120.0(2) . . ? C22 C21 C26 120.4(2) . . ? C22 C21 P1 120.3(2) . . ? C26 C21 P1 119.3(2) . . ? C23 C22 C21 119.4(2) . . ? C23 C22 H22 120.30(14) . . ? C21 C22 H22 120.30(13) . . ? C24 C23 C22 120.4(2) . . ? C24 C23 H23 119.82(14) . . ? C22 C23 H23 119.82(14) . . ? C23 C24 C25 120.4(2) . . ? C23 C24 H24 119.78(14) . . ? C25 C24 H24 119.78(14) . . ? C24 C25 C26 120.2(2) . . ? C24 C25 H25 119.91(14) . . ? C26 C25 H25 119.91(13) . . ? C25 C26 C21 119.2(2) . . ? C25 C26 H26 120.39(13) . . ? C21 C26 H26 120.39(12) . . ? C32 C31 C36 119.9(2) . . ? C32 C31 P1 118.9(2) . . ? C36 C31 P1 121.2(2) . . ? C31 C32 C33 120.0(2) . . ? C31 C32 H32 119.99(13) . . ? C33 C32 H32 120.0(2) . . ? C34 C33 C32 119.8(3) . . ? C34 C33 H33 120.1(2) . . ? C32 C33 H33 120.1(2) . . ? C35 C34 C33 120.7(2) . . ? C35 C34 H34 119.66(14) . . ? C33 C34 H34 119.7(2) . . ? C34 C35 C36 120.0(2) . . ? C34 C35 H35 120.02(14) . . ? C36 C35 H35 120.0(2) . . ? C31 C36 C35 119.6(2) . . ? C31 C36 H36 120.18(14) . . ? C35 C36 H36 120.2(2) . . ? _refine_diff_density_max 0.248 _refine_diff_density_min -0.230 _refine_diff_density_rms 0.057 #============================================================================ data_dada _audit_creation_method SHELXL _chemical_name_systematic ; Amino(triphenyl)phosphonium Hexachloroantimonate ; ... etc. as for the first structure ... _refine_diff_density_max 0.428 _refine_diff_density_min -0.348 _refine_diff_density_rms 0.058 #============================================================================ _eof # End of Crystallographic Information File Appendix E - Distribution and installation of SHELXL-93 ------------------------------------------------------- SHELXL-93 is usually distributed in self-extracting packed form on MSDOS diskette, and contains the following files: shelxl.for - SHELXL source for VAX/VMS 'front end'; this should be compiled without vectorization or optimization. shelxl.f - SHELXL front end for UNIX (and some other) systems. shelxlv.f (or shelxlv.for) - sources for routines which should be fully optimized and/or vectorized. The VAX/VMS and UNIX versions are identical. tyme.c - C routines for the date and time for those UNIX systems which do not provide them (i.e. IBM RS/6000 series). If these are used, all calls from shelxl.f to 'TIME' must be changed to 'TYME' to avoid a clash of names. A special version of 'shelxl.f' (called 'shelxl.ibm') is available in which this has been done. shelxl1.f, shelxl2.f,shelxl3.f and shelxl4.f (or shelxl1.for etc. for VMS). The remaining sources for the main body of the program which should be compiled without vectorization or optimization. The VAX/VMS and UNIX versions are identical. shelxl.hlp - this documentation. This MUST be read before attempting to install or use the programs ! sigi.ins, sigi.hkl, ags4.ins, ags4.hkl - test input files for SHELXL=93 (discussed in detail earlier in this documentation). pdbins.f - essentially computer-independent source of PDBINS (see Appendix B). shelxl.dic - restraints dictionary (currently only for proteins) which is read by PDBINS. This may be used as a model for local 'restraints dictionaries'. ciftab.f - essentially computer-independent source of CIFTAB (see Appendix C). ciftab.def - standard format file for input to CIFTAB. This may be used as a model for users to produce modified tables formats for specific journals etc. ciftab.ang, ciftab.met and ciftab.ger - special format files for tables production using the XTEXT program in the Siemens SHELXTL system. Usually pdbins and ciftab may be compiled and linked with standard compiler options; before installation the comments in these program sources should be consulted ! Compilation on VAX/VMS systems ------------------------------ (a) VaxStation, MicroVAX etc. $ FOR SHELXL,SHELXLV,SHELXL1,SHELXL2,SHELXL3,SHELXL4 $ LINK SHELXL,SHELXLV,SHELXL1,SHELXL2,SHELXL3,SHELXL4 $ SET PROT=(W:E) SHELXL.EXE (b) VAX 9000 (vector processor) etc. $ FORT SHELXL,SHELXL1,SHELXL2,SHELXL3,SHELXL4 $ FORT/VECTOR/ASSUME=(NOACCU,NODUMM)/MATH=FAST/SHOW=ALL SHELXLV $ LINK SHELXL,SHELXLV,SHELXL1,SHELXL2,SHELXL3,SHELXL4 $ SET PROT=(W:E) SHELXL.EXE In both cases the following symbol should also be defined for each session in which the program is used: $ SHELXL :== $ DISK:[USER]SHELXL where DISK and USER define where the file SHELXL.EXE is located, and will need to be replaced by the appropriate names for your system. This line may be included in the LOGIN.COM file for individual users, or - better - a global symbol SHELXL can be defined in the file which is executed when the system is started. Compilation on IRIS (and many other UNIX) systems ------------------------------------------------- For UNIX systems all filenames associated with SHELX should be lower case. The name of the compiler and the optimization switches etc. differ for different systems. There is no need - and it will probably prove counter- productive - to optimize 'shelxl.f', 'shelxl1.f' etc., but it is important to compile 'shelxlv.f' with the highest available optimization level. Typical instructions to compile and link would be: # f77 shelxlv.f -c -O2 # f77 shelxl.f shelxl1.f shelxl2.f shelxl3.f shelxl4.f shelxlv.o -o shelxl The executable program shelxl may then be copied into a directory such as /usr/bin/ for general use (which will require superuser privileges). The UNIX version of SHELXL-93 is able to read the '.ins' and '.hkl' files in either UNIX or DOS format, and may be set up to write the '.res', '.cif' and '.fcf' files in DOS format, so that PC's can access such files via a shared disk without the need for conversion programs such as DOS2UNIX etc. To compile the program with this option the first executable statement in shelxl.f should be KD=CHAR(13) (see the comments in the source). For reasons of efficiency the '.lst' file is always in the local format (it can still be printed directly from a PC using SPRINT - see below). Compilation on IBM RS/6000 series --------------------------------- Since IBM do not (yet) provide FORTRAN-callable DATE and TIME routines, it is necessary to include FORTRAN-callable C routines DATE and TYME provided in the file tyme.c. They may be compiled as follows: # xlc tyme.c -c The rest of the program is then compiled and linked as follows: # xlf shelxlv.f -c -O # xlf shelxl1.f -c -NT50000 -NQ50000 # xlf shelxl2.f -c -NT50000 -NQ50000 # xlf shelxl3.f -c -NT50000 -NQ50000 # xlf shelxl4.f -c -NT50000 -NQ50000 # xlf shelxl.f shelxlv.o shelxl1.o shelxl2.o shelxl3.o shelxl4.o tyme.o -o shelxl Where shelxl.f is a special version in which all the calls to TIME have been changed to TYME; the file 'shelxl.ibm' in which this change has been made may be copied to 'shelxl.f'. Note that the file 'shelxl.ibm' also specifically closes all files before terminating to work around a known system problem. Compilation on Convex computers ------------------------------- 'shelxl.f' must be modified by replacing the statement T=... in subroutine SXTI (in 'shelxl.f') to: T=ETIME(TX) where TX has been declared as a REAL array of dimension 2, i.e. the statement REAL TX(2) is included after the first statement of the subroutine. Compilation on Sun Sparcstations running SUNOS ---------------------------------------------- The same alteration must be made as for Convex, and the -lV77 switch used on the f77 compile/link instruction (n.b. lower case 'L', not digit '1'). Compilation on the Cray Y-MP running UNICOS ------------------------------------------- The line: T=.01*REAL(MCLOCK()) should be changed to: T=SECOND() It is simpler (and safe) to vectorize all routines: # cf77 -l nag -Zp -o shelxl shelxl.f shelxlv.f shelxl1.f shelxl2.f shelxl3.f shelxl4.f Compilation on other computers ------------------------------ Although the UNIX and VAX/VMS versions are almost identical, it will probably prove easier to adapt the UNIX version. The program is standard FORTRAN-77 except for the following routines. Sometimes compiler and linker switches should be set for VAX/VMS-compatibility. Usually it is best to compile and link without optimization first to see if there are unresolved subroutine references. These should only refer to the following non-standard FORTRAN-77 routines, and will have to be replaced by calls to local alternatives. There are a very small number of such calls, and all are to be found in the 'front-end' routines in shelxl.f (or shelxl.for for VMS). A pitfall for the unwary is the possibility that the same names are used for local routines but with different specifications, which can cause the program to appear to compile and link correctly but to abort when started; the most likely culprit is 'TIME'. TIME and DATE - these subroutines should return the current time and date as strings 'HH:MM:SS' and 'DD-MON-YY' (where HH is the hours part of the time as two digits, and MON is a three character abbreviation for the month, etc.). It does not matter which characters are used as separators. MCLOCK - this function should return the current time as a INTEGER number of 1/100 seconds from an arbitrary starting time. The function ETIME (see above) (which returns the number of seconds as a REAL) is a common alternative. IARGC and GETARG - the INTEGER function IARGC should return the number of command line parameters, and the subroutine call GETARG(IARGC(),string) is then used by SHELXL-93 to extract the last of these (it is used to set up all the file names by adding the appropriate extensions). This avoids the confusion over where to start counting parameters ! Precompiled PC versions ----------------------- Two precompiled PC versions are provided. 'SHELXL.EXE' is a 32-bit version which runs in 'protected mode' on 80386SX, 80486SX, 80386DX, 80486DX and Pentium processors. For the first three a numeric coprocessor must also be present. The program contains a built-in (Phar Lap) protected mode loader and so runs as a stand-alone program. It runs as a virtual memory program if the available extended memory is less than about 5MB, which means that about 10MB disk space should be free for scratch files. Since the program is particularly efficient as regards disk input/ouput, it is usually better to leave extended memory free for the program rather than to install a disk cache. On systems with limited physical memory it may be necessary to remove other resident programs and protected mode drivers (in 'AUTOEXEC.BAT' and 'CONFIG.SYS', then reboot). If the program fails to load properly it usually means that either not enough memory is available, or that a memory manager or other resident user of extended memory conflicts and has to be removed first. The Lahey / Phar Lap banner which appears when the program is started gives the amount of extended memory available to the program; it may be suppressed by the statement: SET DOS=-NOSIGNON which can be included in 'AUTOEXEC.BAT'. MSDOS version 5.0 or later is recommended but not absolutely essential. For older personal computers and systems with too little extended memory the 16-bit 'real mode' version 'PCSHELXL.EXE' is also provided. It contains all facilities of 'SHELXL.EXE' but is somewhat slower and has limited memory, so for example is restricted to 300 full-matrix parameters. BLOC or CGLS may be used to refine larger structures, provided that there is room for all atoms, restraints etc.; since the memory allocation is dynamic, there are no individual limits except on the number of least-squares parameters. This version should run on ANY personal computer with an 8088 or compatible CPU and the corresponding coprocessor (not required for 80486DX etc.) and 640 kB of memory. The scratch disk space required depends on the size of the structure; at least 2MB is recommended (a RAM-disk may be used - the scratch files are set up in the current directory). If there is not enough memory to run the program it may be necessary to remove resident drivers (network software is particularly greedy). Although this program should be compatible with MSDOS 2.10 and all subsequent versions, version 5.0 or later is recommended. Although both PC versions are tolerated by MS-WINDOWS and other multitasking interfaces, there is usually a considerable price to pay in terms of performance degradation. If PC's and RISC machines are linked by a NFS network, they may be run using the same files provided that these are in DOS format, because the UNIX version of SHELXL-93 can read DOS format .ins and .hkl files and can be set up to write DOS format .res, .cif and .fcf files (by setting KD=CHAR(13) as the first executable statement in shelxl.f - see comments in the source). If this has been done, all editing may be performed on the PC's; any text editor may be used. For PC's which are connected to a HP Laserjet or compatible printer, a special program SPRINT is provided for printing the documentation and listing files. SPRINT can print both DOS and UNIX format text files (the latter facility is useful for NFS networks). If no filename extension is specified, .lst is assumed. If .lst is given or assumed, the output is compressed; otherwise a margin is left on the left hand side. SPRINT should be able to handle read-only files and printers running out of paper. Examples: SPRINT SHELXL.HLP (to print this manual; similarly READ.ME and REFEREE.MSG) SPRINT AGS4 (to print AGS4.LST in compressed mode after running the test job) Memory requirements, paging etc. -------------------------------- The program uses two large arrays A and B dynamically, so the limits on the size of structure which can be handled are determined by the dimensions of these two arrays and also of the array C; A, B and C are defined as separate COMMON blocks. The standard version of the program is dimensioned for up to 1500 parameters in each full-matrix block and roughly 5000 atoms (assuming a generous number of restraints etc.), and is suitable for a typical (UNIX) workstation (or mainframe) with 8MB or more physical memory; the precompiled (protected mode) PC version 'SHELXL.EXE' is similarly dimensioned. It may be necessary to redimension A, B and C and recompile the program for specific installations, e.g. to fit within a given job category on a mainframe. The highest elements of A and B actually used for the various calculations are printed out by the program (after 'Memory required ='). The program will try to use all available physical (and virtual) memory rather than performing its own disk I/O, thereby achieving longer vector 'runs', which enhances performance on vector and pipelined systems. In some cases, e.g. when a large structure is refined on a MicroVAX or PC with limited physical memory (or allocation of physical memory to a given process in the case of the VAX) this strategy may cause excessive 'paging' and disk I/O. If this happens, the maximum vector run length can be reduced by setting the 4th parameter on the L.S. instruction or by reducing the value of the variable IV in the main program and recompiling; it may also be more efficient to 'block' the refinement or use CGLS (except in the final refinement). Appendix F - Application form ----------------------------- SHELXL-93 USER REGISTRATION FORM | Do not write here ! -------------------------------- | Date sent: Title/Name: | Version: -------------------------------- Full postal address: EMAIL address (if available): Tel: Fax: ---------------------------------------------------------------------------- Please tick ALL relevant boxes, sign and return to: Prof. George Sheldrick, Institut fuer Anorg. Chemie, Tammannstrasse 4, D-37077 Goettingen, Germany. Fax: +49-551-393373; Email: gsheldr @ shelx.uni-ac.gwdg.de ---------------------------------------------------------------------------- SHELXL-93 is supplied ONLY on MSDOS format diskettes, in the form of self- extracting packed files containing MSDOS executables and sources for UNIX and VMS systems, documentation and test data. The programs PDBINS (PDB to SHELXL format conversion) and CIFTAB (tables from SHELXL CIF output) are included. The license fee of DM 4999 for for-profit institutions covers use for an unlimited time on an unlimited number of computers at a specified firm or institution at a single geographical site. SHELXL-93 is currently available free of charge to academics for non-commercial use only; it may prove necessary to change this policy if the license fees for for-profit institutions fail to cover the total costs involved. Academic institutions willing and able to contribute to the costs of developing and distributing the SHELX programs are of course welcome to do so (we suggest DM 99). Please make out checks to "Institut fuer Anorg. Chemie, Prof. Sheldrick". If you wish to pay by direct bank transfer please ask us to send an invoice. ---------------------------------------------------------------------------- [ ] I wish to license SHELXL-93 for use at the following for-profit firm or institution. I agree that within three months I will either destroy all copies of the program in my possession or pay the license fee of DM 4999. ---------------------------------------------------------------------------- [ ] The program will be used exclusively for non-commercial purposes at the following not-for-profit institution only: ---------------------------------------------------------------------------- [ ] Please send me an invoice for DM [ ] Please send me a receipt for the enclosed payment of DM [ ] I agree to cite SHELXL-93 in all publications reporting results obtained using it. [ ] I accept that the author has no liabilities in respect of errors in the programs and documentation. Please supply SHELXL-93 on [ ] 1.44 MB, [ ] 1.2 MB, [ ] either 1.2 or 1.44 MB MSDOS diskettes. [ ] I already possess a copy of SHELXL-93. ---------------------------------------------------------------------------- Signed: Date: